/* ---------------------------------------------------------------------------- * This file was automatically generated by SWIG (http://www.swig.org). * Version 1.3.40 * * 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. * ----------------------------------------------------------------------------- */ #define SWIGPERL #define SWIG_CASTRANK_MODE /* ----------------------------------------------------------------------------- * 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 (__GNUC__ >= 4) || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) # ifndef GCC_HASCLASSVISIBILITY # define GCC_HASCLASSVISIBILITY # 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 /* ----------------------------------------------------------------------------- * 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 and 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 () { if () { *ptr = ; return SWIG_NEWOBJ; } else { *ptr = ; 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 # define SWIG_CheckState(r) (SWIG_IsOK(r) ? 1 : 0) #endif #include #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" == "Class", 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 ||... Return 0 if not equal, 1 if equal */ SWIGRUNTIME int SWIG_TypeEquiv(const char *nb, const char *tb) { int equiv = 0; const char* te = tb + strlen(tb); const char* ne = nb; while (!equiv && *ne) { for (nb = ne; *ne; ++ne) { if (*ne == '|') break; } equiv = (SWIG_TypeNameComp(nb, ne, tb, te) == 0) ? 1 : 0; if (*ne) ++ne; } return equiv; } /* Check type equivalence in a name list like ||... Return 0 if equal, -1 if nb < tb, 1 if nb > tb */ SWIGRUNTIME int SWIG_TypeCompare(const char *nb, const char *tb) { int equiv = 0; const char* te = tb + strlen(tb); const char* ne = nb; while (!equiv && *ne) { for (nb = ne; *ne; ++ne) { if (*ne == '|') break; } equiv = (SWIG_TypeNameComp(nb, ne, tb, te) == 0) ? 1 : 0; if (*ne) ++ne; } return equiv; } /* 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) { register size_t l = 0; register size_t r = iter->size - 1; do { /* since l+r >= 0, we can (>> 1) instead (/ 2) */ register size_t i = (l + r) >> 1; const char *iname = iter->types[i]->name; if (iname) { register 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 { register 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"; register const unsigned char *u = (unsigned char *) ptr; register const unsigned char *eu = u + sz; for (; u != eu; ++u) { register 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) { register unsigned char *u = (unsigned char *) ptr; register const unsigned char *eu = u + sz; for (; u != eu; ++u) { register char d = *(c++); register unsigned char uu; if ((d >= '0') && (d <= '9')) uu = ((d - '0') << 4); else if ((d >= 'a') && (d <= 'f')) uu = ((d - ('a'-10)) << 4); else return (char *) 0; d = *(c++); if ((d >= '0') && (d <= '9')) uu |= (d - '0'); else if ((d >= 'a') && (d <= 'f')) uu |= (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 #include 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 # endif # if !(defined(PERL_VERSION) || (defined(SUBVERSION) && defined(PATCHLEVEL))) # include # 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 #ifdef __cplusplus } #endif /* ----------------------------------------------------------------------------- * error manipulation * ----------------------------------------------------------------------------- */ SWIGINTERN const char* SWIG_Perl_ErrorType(int code) { const char* type = 0; switch(code) { case SWIG_MemoryError: type = "MemoryError"; break; case SWIG_IOError: type = "IOError"; break; case SWIG_RuntimeError: type = "RuntimeError"; break; case SWIG_IndexError: type = "IndexError"; break; case SWIG_TypeError: type = "TypeError"; break; case SWIG_DivisionByZero: type = "ZeroDivisionError"; break; case SWIG_OverflowError: type = "OverflowError"; break; case SWIG_SyntaxError: type = "SyntaxError"; break; case SWIG_ValueError: type = "ValueError"; break; case SWIG_SystemError: type = "SystemError"; break; case SWIG_AttributeError: type = "AttributeError"; break; default: type = "RuntimeError"; } return type; } /* ----------------------------------------------------------------------------- * 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) /* 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() #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(GvSV(PL_errgv),"%s %s\n", 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 */ /* Workaround for bug in perl 5.6.x croak and earlier */ #if (PERL_VERSION < 8) # ifdef PERL_OBJECT # define SWIG_croak_null() SWIG_Perl_croak_null(pPerl) static void SWIG_Perl_croak_null(CPerlObj *pPerl) # else static void SWIG_croak_null() # endif { SV *err=ERRSV; # if (PERL_VERSION < 6) croak("%_", err); # else if (SvOK(err) && !SvROK(err)) croak("%_", err); croak(Nullch); # endif } #else # define SWIG_croak_null() croak(Nullch) #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 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 ( (!iter->type->clientdata && (strcmp(iter->type->name, c) == 0)) || (iter->type->clientdata && (strcmp((char*)iter->type->clientdata, 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)) { *(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); if (!tc) { return SWIG_ERROR; } { int newmemory = 0; *ptr = SWIG_TypeCast(tc,voidptr,&newmemory); if (newmemory == SWIG_CAST_NEW_MEMORY) { assert(own); 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, (char *) 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, (char *) 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 #define swig_create_magic(s,a,b,c) _swig_create_magic(s,a,b,c) #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',(char *) 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) { 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 bool #undef bool #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 #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 /* -------- TYPES TABLE (BEGIN) -------- */ #define SWIGTYPE_p_COORDINATE swig_types[0] #define SWIGTYPE_p_ConcEnt swig_types[1] #define SWIGTYPE_p_FILE swig_types[2] #define SWIGTYPE_p_SOLUTION swig_types[3] #define SWIGTYPE_p_Tree swig_types[4] #define SWIGTYPE_p_bondT swig_types[5] #define SWIGTYPE_p_char swig_types[6] #define SWIGTYPE_p_cpair swig_types[7] #define SWIGTYPE_p_double swig_types[8] #define SWIGTYPE_p_doubleArray swig_types[9] #define SWIGTYPE_p_duplexT swig_types[10] #define SWIGTYPE_p_float swig_types[11] #define SWIGTYPE_p_floatArray swig_types[12] #define SWIGTYPE_p_int swig_types[13] #define SWIGTYPE_p_intArray swig_types[14] #define SWIGTYPE_p_p_char swig_types[15] #define SWIGTYPE_p_p_double swig_types[16] #define SWIGTYPE_p_p_doubleArray swig_types[17] #define SWIGTYPE_p_p_float swig_types[18] #define SWIGTYPE_p_p_floatArray swig_types[19] #define SWIGTYPE_p_p_int swig_types[20] #define SWIGTYPE_p_p_intArray swig_types[21] #define SWIGTYPE_p_p_p_char swig_types[22] #define SWIGTYPE_p_p_p_short swig_types[23] #define SWIGTYPE_p_p_p_unsigned_short swig_types[24] #define SWIGTYPE_p_p_plist swig_types[25] #define SWIGTYPE_p_p_short swig_types[26] #define SWIGTYPE_p_p_void swig_types[27] #define SWIGTYPE_p_paramT swig_types[28] #define SWIGTYPE_p_path_t swig_types[29] #define SWIGTYPE_p_plist swig_types[30] #define SWIGTYPE_p_short swig_types[31] #define SWIGTYPE_p_swString swig_types[32] #define SWIGTYPE_p_unsigned_int swig_types[33] #define SWIGTYPE_p_unsigned_short swig_types[34] #define SWIGTYPE_p_void swig_types[35] static swig_type_info *swig_types[37]; static swig_module_info swig_module = {swig_types, 36, 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_RNA #define SWIG_name "RNAc::boot_RNA" #define SWIG_prefix "RNAc::" #define SWIGVERSION 0x010340 #define SWIG_VERSION SWIGVERSION #define SWIG_as_voidptr(a) (void *)((const void *)(a)) #define SWIG_as_voidptrptr(a) ((void)SWIG_as_voidptr(*a),(void**)(a)) #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 #include "../H/utils.h" #include "../H/fold_vars.h" #undef fold #include "../H/fold.h" #include "../H/cofold.h" #include "../H/part_func.h" #include "../H/part_func_co.h" #include "../H/naview.h" #include "../H/PS_dot.h" #include "../H/inverse.h" #include "../H/RNAstruct.h" #include "../H/treedist.h" #include "../H/stringdist.h" #include "../H/profiledist.h" #include "../H/dist_vars.h" #include "../H/pair_mat.h" #include "../H/subopt.h" #include "../H/energy_const.h" #include "../H/params.h" #include "../H/duplex.h" #include "../H/alifold.h" #include "../H/aln_util.h" #include "../H/findpath.h" #include "../H/Lfold.h" #include "../H/data_structures.h" #include "../H/read_epars.h" static int *new_intP(size_t nelements) { return (int *)malloc((nelements)*sizeof(int)); } static void delete_intP(int *ary) { free((char*)ary); } static int intP_getitem(int *ary, size_t index) { return ary[index]; } static void intP_setitem(int *ary, size_t index, int value) { ary[index] = value; } 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 = 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 #include 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)) { if (val) *val = SvUV(obj); return SWIG_OK; } else if (SvIOK(obj)) { long v = SvIV(obj); if (v >= 0) { 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 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; } SWIGINTERNINLINE int SWIG_AsVal_size_t SWIG_PERL_DECL_ARGS_2(SV * obj, size_t *val) { unsigned long v; int res = SWIG_AsVal_unsigned_SS_long SWIG_PERL_CALL_ARGS_2(obj, val ? &v : 0); if (SWIG_IsOK(res) && val) *val = (size_t)(v); return res; } SWIGINTERNINLINE SV * SWIG_From_long SWIG_PERL_DECL_ARGS_1(long value) { SV *obj = sv_newmortal(); sv_setiv(obj, (IV) value); return obj; } SWIGINTERNINLINE SV * SWIG_From_int SWIG_PERL_DECL_ARGS_1(int value) { return SWIG_From_long SWIG_PERL_CALL_ARGS_1(value); } #include #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 SWIGINTERN int SWIG_AsVal_long SWIG_PERL_DECL_ARGS_2(SV *obj, long* val) { if (SvIOK(obj)) { if (val) *val = SvIV(obj); return SWIG_OK; } 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; } 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 = (int)(v); } } return res; } typedef int intArray; SWIGINTERN intArray *new_intArray(size_t nelements){ return (int *)malloc((nelements)*sizeof(int)); } SWIGINTERN void delete_intArray(intArray *self){ free((char*)self); } SWIGINTERN int intArray_getitem(intArray *self,size_t index){ return self[index]; } SWIGINTERN void intArray_setitem(intArray *self,size_t index,int value){ self[index] = value; } SWIGINTERN int *intArray_cast(intArray *self){ return self; } SWIGINTERN intArray *intArray_frompointer(int *t){ return (intArray *)(t); } static float *new_floatP(size_t nelements) { return (float *)malloc((nelements)*sizeof(float)); } static void delete_floatP(float *ary) { free((char*)ary); } static float floatP_getitem(float *ary, size_t index) { return ary[index]; } static void floatP_setitem(float *ary, size_t index, float value) { ary[index] = value; } SWIGINTERNINLINE SV * SWIG_From_double SWIG_PERL_DECL_ARGS_1(double value) { SV *obj = sv_newmortal(); sv_setnv(obj, value); return obj; } SWIGINTERNINLINE SV * SWIG_From_float SWIG_PERL_DECL_ARGS_1(float value) { return SWIG_From_double SWIG_PERL_CALL_ARGS_1(value); } SWIGINTERN int SWIG_AsVal_float SWIG_PERL_DECL_ARGS_2(SV * obj, float *val) { double v; int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(obj, &v); if (SWIG_IsOK(res)) { if ((v < -FLT_MAX || v > FLT_MAX)) { return SWIG_OverflowError; } else { if (val) *val = (float)(v); } } return res; } typedef float floatArray; SWIGINTERN floatArray *new_floatArray(size_t nelements){ return (float *)malloc((nelements)*sizeof(float)); } SWIGINTERN void delete_floatArray(floatArray *self){ free((char*)self); } SWIGINTERN float floatArray_getitem(floatArray *self,size_t index){ return self[index]; } SWIGINTERN void floatArray_setitem(floatArray *self,size_t index,float value){ self[index] = value; } SWIGINTERN float *floatArray_cast(floatArray *self){ return self; } SWIGINTERN floatArray *floatArray_frompointer(float *t){ return (floatArray *)(t); } static double *new_doubleP(size_t nelements) { return (double *)malloc((nelements)*sizeof(double)); } static void delete_doubleP(double *ary) { free((char*)ary); } static double doubleP_getitem(double *ary, size_t index) { return ary[index]; } static void doubleP_setitem(double *ary, size_t index, double value) { ary[index] = value; } typedef double doubleArray; SWIGINTERN doubleArray *new_doubleArray(size_t nelements){ return (double *)malloc((nelements)*sizeof(double)); } SWIGINTERN void delete_doubleArray(doubleArray *self){ free((char*)self); } SWIGINTERN double doubleArray_getitem(doubleArray *self,size_t index){ return self[index]; } SWIGINTERN void doubleArray_setitem(doubleArray *self,size_t index,double value){ self[index] = value; } SWIGINTERN double *doubleArray_cast(doubleArray *self){ return self; } SWIGINTERN doubleArray *doubleArray_frompointer(double *t){ return (doubleArray *)(t); } static unsigned short *new_ushortP(size_t nelements) { return (unsigned short *)malloc((nelements)*sizeof(unsigned short)); } static void delete_ushortP(unsigned short *ary) { free((char*)ary); } static unsigned short ushortP_getitem(unsigned short *ary, size_t index) { return ary[index]; } static void ushortP_setitem(unsigned short *ary, size_t index, unsigned short value) { ary[index] = value; } SWIGINTERNINLINE SV * SWIG_From_unsigned_SS_long SWIG_PERL_DECL_ARGS_1(unsigned long value) { SV *obj = sv_newmortal(); sv_setuv(obj, (UV) value); return obj; } SWIGINTERNINLINE SV * SWIG_From_unsigned_SS_short SWIG_PERL_DECL_ARGS_1(unsigned short value) { return SWIG_From_unsigned_SS_long SWIG_PERL_CALL_ARGS_1(value); } SWIGINTERN int SWIG_AsVal_unsigned_SS_short SWIG_PERL_DECL_ARGS_2(SV * obj, unsigned short *val) { unsigned long v; int res = SWIG_AsVal_unsigned_SS_long SWIG_PERL_CALL_ARGS_2(obj, &v); if (SWIG_IsOK(res)) { if ((v > USHRT_MAX)) { return SWIG_OverflowError; } else { if (val) *val = (unsigned short)(v); } } return res; } static short *new_shortP(size_t nelements) { return (short *)malloc((nelements)*sizeof(short)); } static void delete_shortP(short *ary) { free((char*)ary); } static short shortP_getitem(short *ary, size_t index) { return ary[index]; } static void shortP_setitem(short *ary, size_t index, short value) { ary[index] = value; } SWIGINTERNINLINE SV * SWIG_From_short SWIG_PERL_DECL_ARGS_1(short value) { return SWIG_From_long SWIG_PERL_CALL_ARGS_1(value); } SWIGINTERN int SWIG_AsVal_short SWIG_PERL_DECL_ARGS_2(SV * obj, short *val) { long v; int res = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(obj, &v); if (SWIG_IsOK(res)) { if ((v < SHRT_MIN || v > SHRT_MAX)) { return SWIG_OverflowError; } else { if (val) *val = (short)(v); } } return res; } typedef struct SWIGCDATA { char *data; size_t len; } SWIGCDATA; static SWIGCDATA cdata_void(void *ptr, size_t nelements) { SWIGCDATA d; d.data = (char *) ptr; d.len = nelements; return d; } 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; } char *my_fold(char *string, char *constraints, float *energy) { char *struc; struc = calloc(strlen(string)+1,sizeof(char)); if (constraints && fold_constrained) strncpy(struc, constraints, strlen(string)); *energy = fold(string, struc); if (constraints) strncpy(constraints, struc, strlen(constraints)); return(struc); } 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 = (char *)memcpy((char *)malloc((size)*sizeof(char)), 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; } SWIGINTERNINLINE SV * SWIG_FromCharPtr(const char *cptr) { return SWIG_FromCharPtrAndSize(cptr, (cptr ? strlen(cptr) : 0)); } char *my_cofold(char *string, char *constraints, float *energy) { char *struc; struc = calloc(strlen(string)+1,sizeof(char)); if (constraints && fold_constrained) strncpy(struc, constraints, strlen(string)); if (cut_point > strlen(string)) { cut_point = -1; } *energy = cofold(string, struc); if (constraints) strncpy(constraints, struc, strlen(constraints)); return(struc); } char *my_pf_fold(char *string, char *constraints, float *energy) { char *struc; struc = calloc(strlen(string)+1,sizeof(char)); if (constraints && fold_constrained) strncpy(struc, constraints, strlen(string)); *energy = pf_fold(string, struc); if (constraints) strncpy(constraints, struc, strlen(constraints)); return(struc); } 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 = (unsigned int)(v); } } return res; } SWIGINTERNINLINE SV * SWIG_From_char SWIG_PERL_DECL_ARGS_1(char c) { return SWIG_FromCharPtrAndSize(&c,1); } char *my_co_pf_fold(char *string, char *constraints, float *FA, float *FB, float *FcAB, float *FAB) { char *struc; float en; cofoldF temp; struc = calloc(strlen(string)+1,sizeof(char)); if (constraints && fold_constrained) strncpy(struc, constraints, strlen(string)); temp=co_pf_fold(string, struc); *FAB = temp.FAB; *FcAB = temp.FcAB; *FA = temp.FA; *FB = temp.FB; if (constraints) strncpy(constraints, struc, strlen(constraints)); return(struc); } void my_get_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, double A0, double B0, double *AB, double *AA, double *BB, double *A, double *B) { ConcEnt *temp; double *concis; concis = (double *)calloc(3,sizeof(double)); concis[0]=A0; concis[1]=B0; temp=get_concentrations(FcAB,FcAA,FcBB,FEA,FEB,concis); *AB=temp->ABc; *AA=temp->AAc; *BB=temp->BBc; *A=temp->Ac; *B=temp->Bc; free(concis); free(temp); return; } char *my_inverse_fold(char *start, const char *target, float *cost) { char *seq; int n; n = strlen(target); seq = random_string(n, symbolset); if (start) strncpy(seq, start, strlen(start)); *cost = inverse_fold(seq, target); if (start) /* for backward compatibility modify start */ strncpy(start, seq, strlen(start)); return(seq); } char *my_inverse_pf_fold(char *start, const char *target, float *cost) { char *seq; int n; n = strlen(target); seq = random_string(n, symbolset); if (start) strncpy(seq, start, n); *cost = inverse_pf_fold(seq, target); if (start) /* for backward compatibility modify start */ strncpy(start, seq, strlen(start)); return(seq); } SWIGINTERN int SWIG_AsCharArray(SV * obj, char *val, size_t size) { char* cptr = 0; size_t csize = 0; int alloc = SWIG_OLDOBJ; int res = SWIG_AsCharPtrAndSize(obj, &cptr, &csize, &alloc); if (SWIG_IsOK(res)) { if ((csize == size + 1) && cptr && !(cptr[csize-1])) --csize; if (csize <= size) { if (val) { if (csize) memcpy(val, cptr, csize*sizeof(char)); if (csize < size) memset(val + csize, 0, (size - csize)*sizeof(char)); } if (alloc == SWIG_NEWOBJ) { free((char*)cptr); res = SWIG_DelNewMask(res); } return res; } if (alloc == SWIG_NEWOBJ) free((char*)cptr); } return SWIG_TypeError; } SWIGINTERN int SWIG_AsVal_char SWIG_PERL_DECL_ARGS_2(SV * obj, char *val) { int res = SWIG_AsCharArray(obj, val, 1); if (!SWIG_IsOK(res)) { long v; res = SWIG_AddCast(SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(obj, &v)); if (SWIG_IsOK(res)) { if ((CHAR_MIN <= v) && (v <= CHAR_MAX)) { if (val) *val = (char)(v); } else { res = SWIG_OverflowError; } } } return res; } char *my_alifold(char **strings, char *constraints, float *energy) { char *struc; struc = calloc(strlen(strings[0])+1,sizeof(char)); if (constraints && fold_constrained) strncpy(struc, constraints, strlen(strings[0])); *energy = alifold(strings, struc); if (constraints) strncpy(constraints, struc, strlen(constraints)); return(struc); } SWIGINTERN COORDINATE *COORDINATE_get(COORDINATE *self,int i){ return self+i; } COORDINATE *get_xy_coordinates(const char *structure){ int i; short *table = make_pair_table(structure); short length = (short) strlen(structure); COORDINATE *coords = (COORDINATE *) space((length+1)*sizeof(COORDINATE)); float *X = (float *) space((length+1)*sizeof(float)); float *Y = (float *) space((length+1)*sizeof(float)); if (rna_plot_type == 0) simple_xy_coordinates(table, X, Y); else naview_xy_coordinates(table, X, Y); for(i=0;i<=length;i++){ coords[i].X = X[i]; coords[i].Y = Y[i]; } free(table); free(X); free(Y); return(coords); } SWIGINTERN SOLUTION *SOLUTION_get(SOLUTION *self,int i){ // static int size=-1; // if (size<0) { // SOLUTION *s; // for (s=self; s->structure; s++); // size= (int) (s-self); // } // if (i>=size) { // warn("value out of range"); // return NULL; // } return self+i; } SWIGINTERN int SOLUTION_size(SOLUTION *self){ SOLUTION *s; for (s=self; s->structure; s++); return (int)(s-self); } SWIGINTERN void delete_SOLUTION(SOLUTION *self){ SOLUTION *s; for (s=self; s->structure; s++) free(s->structure); free(self); } double get_pr(int i, int j) { int ii; if (i>j) {ii=i; i=j; j=ii;} return pr[iindx[i]-j]; } 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); } void *deref_any(void **ptr, int index) { /* dereference arbitray pointer */ return (void *) ptr[index]; } char *get_aligned_line(int i) { i = i % 2; return aligned_line[i]; } short *make_loop_index(const char *structure) { /* number each position by which loop it belongs to (positions start at 0) */ int i,hx,l,nl; int length; short *stack; short *loop; length = strlen(structure); stack = (short *) space(sizeof(short)*(length+1)); loop = (short *) space(sizeof(short)*(length+2)); hx=l=nl=0; for (i=0; i0) l = loop[stack[hx-1]]; /* index of enclosing loop */ else l=0; /* external loop has index 0 */ if (hx<0) { fprintf(stderr, "%s\n", structure); nrerror("unbalanced brackets in make_pair_table"); } } } free(stack); return loop; } float energy_of_move(const char *string, char *structure, int mi, int mj) { extern int energy_of_struct_pt(const char *string, short * ptable, short *s, short *s1); #define ILLEGAL 999.; int i,j,hx,l,nl; int length; short *stack, *table, *loop; short *S; int energy; if (mj<0) { if ((structure[-mi]!='(') || (structure[-mj]!=')')) return 1001; /* illegal delete pair */ } else if ((structure[mi]!='.') || (structure[mj]!='.')) return 1002; /* illegal add pair */ /* make the pair table and loop index l*/ length = strlen(structure); stack = (short *) space(sizeof(short)*(length+1)); loop = (short *) space(sizeof(short)*(length+2)); table = (short *) space(sizeof(short)*(length+2)); table[0] = length; hx=l=nl=0; for (i=1; i<=length; i++) { if (structure[i-1] == '(') { nl++; l=nl; stack[hx++]=i; } loop[i]=l; if (structure[i-1] ==')') { j=stack[--hx]; if (hx>0) l = loop[stack[hx-1]]; /* index of enclosing loop */ else l=0; /* external loop has index 0 */ if (hx<0) { fprintf(stderr, "%s\n", structure); nrerror("unbalanced brackets in energy_of_move"); } table[i]=j; table[j]=i; } } if (hx!=0) { fprintf(stderr, "%s\n", structure); nrerror("unbalanced brackets in energy_of_move"); } if (loop[abs(mi)+1] != loop[abs(mj)+1]) { /* not in same loop => illegal */ free(stack); free(loop); free(table); return 1003.; } /* if we get here the move is legal */ if (mj<0) { /* delete pair */ structure[-mi] = '.'; structure[-mj] = '.'; table[-mi+1] = table[-mj+1] = 0; } else { /* insert pair */ structure[mi] = '('; structure[mj] = ')'; table[mi+1] = mj+1; table[mj+1] = mi+1; } S = (short *) space(sizeof(short)*(length+1)); S[0] = length; for (i=1; i<=length; i++) { char *pos; pos = strchr(Law_and_Order, string[i-1]); if (pos==NULL) S[i]=0; else S[i] = pos-Law_and_Order; } energy = energy_of_struct_pt(string, table, S, S); free(S); free(stack); free(loop); free(table); return (float) energy/100.; } short *encode_seq(char *sequence) { unsigned int i,l; short *S; l = strlen(sequence); S = (short *) space(sizeof(short)*(l+2)); S[0] = (short) l; /* make numerical encoding of sequence */ for (i=1; i<=l; i++) S[i]= (short) encode_char(toupper(sequence[i-1])); /* for circular folding add first base at position n+1 */ S[l+1] = S[1]; return S; } #ifdef __cplusplus extern "C" { #endif #ifdef PERL_OBJECT #define MAGIC_CLASS _wrap_RNA_var:: class _wrap_RNA_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; } SWIGCLASS_STATIC int _wrap_logML_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""logML""' of type '""int""'"); } logML = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_logML_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(logML))) ; return 1; } SWIGCLASS_STATIC int _wrap_uniq_ML_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""uniq_ML""' of type '""int""'"); } uniq_ML = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_uniq_ML_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(uniq_ML))) ; return 1; } SWIGCLASS_STATIC int _wrap_cut_point_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""cut_point""' of type '""int""'"); } cut_point = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_cut_point_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(cut_point))) ; return 1; } SWIGCLASS_STATIC int _wrap_eos_debug_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""eos_debug""' of type '""int""'"); } eos_debug = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_eos_debug_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(eos_debug))) ; return 1; } SWIGCLASS_STATIC int _wrap_st_back_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""st_back""' of type '""int""'"); } st_back = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_st_back_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(st_back))) ; return 1; } SWIGCLASS_STATIC int _wrap_mirnatog_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""mirnatog""' of type '""int""'"); } mirnatog = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_mirnatog_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(mirnatog))) ; return 1; } SWIGCLASS_STATIC int _wrap_F_monomer_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { double *inp = 0; int res = SWIG_ConvertPtr(sv, SWIG_as_voidptrptr(&inp), SWIGTYPE_p_double, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""F_monomer""' of type '""double [2]""'"); } else if (inp) { size_t ii = 0; for (; ii < (size_t)2; ++ii) F_monomer[ii] = inp[ii]; } else { SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""F_monomer""' of type '""double [2]""'"); } } fail: return 1; } SWIGCLASS_STATIC int _wrap_F_monomer_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(F_monomer)); return 1; } SWIGCLASS_STATIC int _wrap_symbolset_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { char *cptr = 0; size_t csize = 0; int alloc = SWIG_NEWOBJ; int res = SWIG_AsCharPtrAndSize(sv, &cptr, &csize, &alloc); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""symbolset""' of type '""char *""'"); } if (symbolset) free((char*)symbolset); if (alloc == SWIG_NEWOBJ) { symbolset = cptr; } else { symbolset = csize ? (char *)(char *)memcpy((char *)malloc((csize)*sizeof(char)), cptr, sizeof(char)*(csize)) : 0; } } fail: return 1; } SWIGCLASS_STATIC int _wrap_symbolset_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_FromCharPtr(symbolset)) ; return 1; } SWIGCLASS_STATIC int _wrap_final_cost_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { float val; int res = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""final_cost""' of type '""float""'"); } final_cost = (float)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_final_cost_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(final_cost))) ; return 1; } SWIGCLASS_STATIC int _wrap_give_up_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""give_up""' of type '""int""'"); } give_up = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_give_up_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(give_up))) ; return 1; } SWIGCLASS_STATIC int _wrap_inv_verbose_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""inv_verbose""' of type '""int""'"); } inv_verbose = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_inv_verbose_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(inv_verbose))) ; return 1; } SWIGCLASS_STATIC int _wrap_fold_constrained_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""fold_constrained""' of type '""int""'"); } fold_constrained = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_fold_constrained_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(fold_constrained))) ; return 1; } SWIGCLASS_STATIC int _wrap_noLonelyPairs_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""noLonelyPairs""' of type '""int""'"); } noLonelyPairs = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_noLonelyPairs_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(noLonelyPairs))) ; return 1; } SWIGCLASS_STATIC int _wrap_dangles_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""dangles""' of type '""int""'"); } dangles = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_dangles_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(dangles))) ; return 1; } SWIGCLASS_STATIC int _wrap_noGU_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""noGU""' of type '""int""'"); } noGU = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_noGU_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(noGU))) ; return 1; } SWIGCLASS_STATIC int _wrap_no_closingGU_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""no_closingGU""' of type '""int""'"); } no_closingGU = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_no_closingGU_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(no_closingGU))) ; return 1; } SWIGCLASS_STATIC int _wrap_tetra_loop_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""tetra_loop""' of type '""int""'"); } tetra_loop = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_tetra_loop_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(tetra_loop))) ; return 1; } SWIGCLASS_STATIC int _wrap_energy_set_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""energy_set""' of type '""int""'"); } energy_set = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_energy_set_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(energy_set))) ; return 1; } SWIGCLASS_STATIC int _wrap_circ_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""circ""' of type '""int""'"); } circ = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_circ_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(circ))) ; return 1; } SWIGCLASS_STATIC int _wrap_csv_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""csv""' of type '""int""'"); } csv = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_csv_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(csv))) ; return 1; } SWIGCLASS_STATIC int _wrap_oldAliEn_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""oldAliEn""' of type '""int""'"); } oldAliEn = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_oldAliEn_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(oldAliEn))) ; return 1; } SWIGCLASS_STATIC int _wrap_ribo_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""ribo""' of type '""int""'"); } ribo = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_ribo_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(ribo))) ; return 1; } SWIGCLASS_STATIC int _wrap_RibosumFile_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { char *cptr = 0; size_t csize = 0; int alloc = SWIG_NEWOBJ; int res = SWIG_AsCharPtrAndSize(sv, &cptr, &csize, &alloc); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""RibosumFile""' of type '""char *""'"); } if (RibosumFile) free((char*)RibosumFile); if (alloc == SWIG_NEWOBJ) { RibosumFile = cptr; } else { RibosumFile = csize ? (char *)(char *)memcpy((char *)malloc((csize)*sizeof(char)), cptr, sizeof(char)*(csize)) : 0; } } fail: return 1; } SWIGCLASS_STATIC int _wrap_RibosumFile_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_FromCharPtr(RibosumFile)) ; return 1; } SWIGCLASS_STATIC int _wrap_nonstandards_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { char *cptr = 0; size_t csize = 0; int alloc = SWIG_NEWOBJ; int res = SWIG_AsCharPtrAndSize(sv, &cptr, &csize, &alloc); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""nonstandards""' of type '""char *""'"); } if (nonstandards) free((char*)nonstandards); if (alloc == SWIG_NEWOBJ) { nonstandards = cptr; } else { nonstandards = csize ? (char *)(char *)memcpy((char *)malloc((csize)*sizeof(char)), cptr, sizeof(char)*(csize)) : 0; } } fail: return 1; } SWIGCLASS_STATIC int _wrap_nonstandards_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_FromCharPtr(nonstandards)) ; return 1; } SWIGCLASS_STATIC int _wrap_temperature_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { double val; int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""temperature""' of type '""double""'"); } temperature = (double)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_temperature_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(temperature))) ; return 1; } SWIGCLASS_STATIC int _wrap_james_rule_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""james_rule""' of type '""int""'"); } james_rule = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_james_rule_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(james_rule))) ; return 1; } SWIGCLASS_STATIC int _wrap_base_pair_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { void *argp = 0; int res = SWIG_ConvertPtr(sv, &argp, SWIGTYPE_p_bondT, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""base_pair""' of type '""bondT *""'"); } base_pair = (bondT *)(argp); } fail: return 1; } SWIGCLASS_STATIC int _wrap_base_pair_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(base_pair)); return 1; } SWIGCLASS_STATIC int _wrap_pr_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { void *argp = 0; int res = SWIG_ConvertPtr(sv, &argp, SWIGTYPE_p_double, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""pr""' of type '""double *""'"); } pr = (double *)(argp); } fail: return 1; } SWIGCLASS_STATIC int _wrap_pr_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(pr)); return 1; } SWIGCLASS_STATIC int _wrap_iindx_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { void *argp = 0; int res = SWIG_ConvertPtr(sv, &argp, SWIGTYPE_p_int, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""iindx""' of type '""int *""'"); } iindx = (int *)(argp); } fail: return 1; } SWIGCLASS_STATIC int _wrap_iindx_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(iindx)); return 1; } SWIGCLASS_STATIC int _wrap_pf_scale_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { double val; int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""pf_scale""' of type '""double""'"); } pf_scale = (double)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_pf_scale_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(pf_scale))) ; return 1; } SWIGCLASS_STATIC int _wrap_do_backtrack_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""do_backtrack""' of type '""int""'"); } do_backtrack = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_do_backtrack_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(do_backtrack))) ; return 1; } SWIGCLASS_STATIC int _wrap_backtrack_type_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { char val; int res = SWIG_AsVal_char SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""backtrack_type""' of type '""char""'"); } backtrack_type = (char)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_backtrack_type_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_char SWIG_PERL_CALL_ARGS_1((char)(backtrack_type))) ; return 1; } SWIGCLASS_STATIC int _wrap_cv_fact_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { double val; int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""cv_fact""' of type '""double""'"); } cv_fact = (double)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_cv_fact_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(cv_fact))) ; return 1; } SWIGCLASS_STATIC int _wrap_nc_fact_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { double val; int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""nc_fact""' of type '""double""'"); } nc_fact = (double)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_nc_fact_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(nc_fact))) ; return 1; } SWIGCLASS_STATIC int _wrap_subopt_sorted_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""subopt_sorted""' of type '""int""'"); } subopt_sorted = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_subopt_sorted_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(subopt_sorted))) ; return 1; } SWIGCLASS_STATIC int _wrap_loop_size_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int *inp = 0; int res = SWIG_ConvertPtr(sv, SWIG_as_voidptrptr(&inp), SWIGTYPE_p_int, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""loop_size""' of type '""int [1000]""'"); } else if (inp) { size_t ii = 0; for (; ii < (size_t)1000; ++ii) loop_size[ii] = inp[ii]; } else { SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""loop_size""' of type '""int [1000]""'"); } } fail: return 1; } SWIGCLASS_STATIC int _wrap_loop_size_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(loop_size)); return 1; } SWIGCLASS_STATIC int _wrap_helix_size_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int *inp = 0; int res = SWIG_ConvertPtr(sv, SWIG_as_voidptrptr(&inp), SWIGTYPE_p_int, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""helix_size""' of type '""int [1000]""'"); } else if (inp) { size_t ii = 0; for (; ii < (size_t)1000; ++ii) helix_size[ii] = inp[ii]; } else { SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""helix_size""' of type '""int [1000]""'"); } } fail: return 1; } SWIGCLASS_STATIC int _wrap_helix_size_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(helix_size)); return 1; } SWIGCLASS_STATIC int _wrap_loop_degree_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int *inp = 0; int res = SWIG_ConvertPtr(sv, SWIG_as_voidptrptr(&inp), SWIGTYPE_p_int, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""loop_degree""' of type '""int [1000]""'"); } else if (inp) { size_t ii = 0; for (; ii < (size_t)1000; ++ii) loop_degree[ii] = inp[ii]; } else { SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""loop_degree""' of type '""int [1000]""'"); } } fail: return 1; } SWIGCLASS_STATIC int _wrap_loop_degree_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(loop_degree)); return 1; } SWIGCLASS_STATIC int _wrap_loops_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""loops""' of type '""int""'"); } loops = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_loops_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(loops))) ; return 1; } SWIGCLASS_STATIC int _wrap_unpaired_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""unpaired""' of type '""int""'"); } unpaired = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_unpaired_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(unpaired))) ; return 1; } SWIGCLASS_STATIC int _wrap_pairs_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""pairs""' of type '""int""'"); } pairs = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_pairs_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(pairs))) ; return 1; } SWIGCLASS_STATIC int _wrap_edit_backtrack_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""edit_backtrack""' of type '""int""'"); } edit_backtrack = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_edit_backtrack_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(edit_backtrack))) ; return 1; } SWIGCLASS_STATIC int _wrap_aligned_line_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { char * *inp = 0; int res = SWIG_ConvertPtr(sv, SWIG_as_voidptrptr(&inp), SWIGTYPE_p_p_char, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""aligned_line""' of type '""char *[2]""'"); } else if (inp) { size_t ii = 0; for (; ii < (size_t)2; ++ii) aligned_line[ii] = inp[ii]; } else { SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""aligned_line""' of type '""char *[2]""'"); } } fail: return 1; } SWIGCLASS_STATIC int _wrap_aligned_line_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(aligned_line)); return 1; } SWIGCLASS_STATIC int _wrap_cost_matrix_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""cost_matrix""' of type '""int""'"); } cost_matrix = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_cost_matrix_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(cost_matrix))) ; return 1; } SWIGCLASS_STATIC int _wrap_xsubi_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { unsigned short *inp = 0; int res = SWIG_ConvertPtr(sv, SWIG_as_voidptrptr(&inp), SWIGTYPE_p_unsigned_short, 0 ); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""xsubi""' of type '""unsigned short [3]""'"); } else if (inp) { size_t ii = 0; for (; ii < (size_t)3; ++ii) xsubi[ii] = inp[ii]; } else { SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""xsubi""' of type '""unsigned short [3]""'"); } } fail: return 1; } SWIGCLASS_STATIC int _wrap_xsubi_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setiv(SvRV(sv),PTR2IV(xsubi)); return 1; } SWIGCLASS_STATIC int _wrap_rna_plot_type_set(pTHX_ SV* sv, MAGIC * SWIGUNUSEDPARM(mg)) { MAGIC_PPERL { int val; int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(sv, &val); if (!SWIG_IsOK(res)) { SWIG_exception_fail(SWIG_ArgError(res), "in variable '""rna_plot_type""' of type '""int""'"); } rna_plot_type = (int)(val); } fail: return 1; } SWIGCLASS_STATIC int _wrap_rna_plot_type_get(pTHX_ SV *sv, MAGIC *SWIGUNUSEDPARM(mg)) { MAGIC_PPERL sv_setsv(sv,SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(rna_plot_type))) ; return 1; } #ifdef PERL_OBJECT }; #endif #ifdef __cplusplus } #endif #ifdef __cplusplus extern "C" { #endif XS(_wrap_new_intP) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; int *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_intP(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_intP" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (int *)new_intP(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_int, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_intP) { { int *arg1 = (int *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_intP(ary);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_intP" "', argument " "1"" of type '" "int *""'"); } arg1 = (int *)(argp1); delete_intP(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_intP_getitem) { { int *arg1 = (int *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: intP_getitem(ary,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "intP_getitem" "', argument " "1"" of type '" "int *""'"); } arg1 = (int *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "intP_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (int)intP_getitem(arg1,arg2); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_intP_setitem) { { int *arg1 = (int *) 0 ; size_t arg2 ; int arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: intP_setitem(ary,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "intP_setitem" "', argument " "1"" of type '" "int *""'"); } arg1 = (int *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "intP_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "intP_setitem" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); intP_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_intArray) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; intArray *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_intArray(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_intArray" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (intArray *)new_intArray(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_intArray, SWIG_OWNER | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_intArray) { { intArray *arg1 = (intArray *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_intArray(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_intArray, SWIG_POINTER_DISOWN | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_intArray" "', argument " "1"" of type '" "intArray *""'"); } arg1 = (intArray *)(argp1); delete_intArray(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_intArray_getitem) { { intArray *arg1 = (intArray *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: intArray_getitem(self,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_intArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "intArray_getitem" "', argument " "1"" of type '" "intArray *""'"); } arg1 = (intArray *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "intArray_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (int)intArray_getitem(arg1,arg2); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_intArray_setitem) { { intArray *arg1 = (intArray *) 0 ; size_t arg2 ; int arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: intArray_setitem(self,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_intArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "intArray_setitem" "', argument " "1"" of type '" "intArray *""'"); } arg1 = (intArray *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "intArray_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "intArray_setitem" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); intArray_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_intArray_cast) { { intArray *arg1 = (intArray *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; int *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: intArray_cast(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_intArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "intArray_cast" "', argument " "1"" of type '" "intArray *""'"); } arg1 = (intArray *)(argp1); result = (int *)intArray_cast(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_int, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_intArray_frompointer) { { int *arg1 = (int *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; intArray *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: intArray_frompointer(t);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "intArray_frompointer" "', argument " "1"" of type '" "int *""'"); } arg1 = (int *)(argp1); result = (intArray *)intArray_frompointer(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_intArray, 0 | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_floatP) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; float *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_floatP(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_floatP" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (float *)new_floatP(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_float, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_floatP) { { float *arg1 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_floatP(ary);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_floatP" "', argument " "1"" of type '" "float *""'"); } arg1 = (float *)(argp1); delete_floatP(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_floatP_getitem) { { float *arg1 = (float *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: floatP_getitem(ary,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "floatP_getitem" "', argument " "1"" of type '" "float *""'"); } arg1 = (float *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "floatP_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (float)floatP_getitem(arg1,arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_floatP_setitem) { { float *arg1 = (float *) 0 ; size_t arg2 ; float arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; float val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: floatP_setitem(ary,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "floatP_setitem" "', argument " "1"" of type '" "float *""'"); } arg1 = (float *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "floatP_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "floatP_setitem" "', argument " "3"" of type '" "float""'"); } arg3 = (float)(val3); floatP_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_floatArray) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; floatArray *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_floatArray(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_floatArray" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (floatArray *)new_floatArray(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_floatArray, SWIG_OWNER | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_floatArray) { { floatArray *arg1 = (floatArray *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_floatArray(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_floatArray, SWIG_POINTER_DISOWN | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_floatArray" "', argument " "1"" of type '" "floatArray *""'"); } arg1 = (floatArray *)(argp1); delete_floatArray(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_floatArray_getitem) { { floatArray *arg1 = (floatArray *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: floatArray_getitem(self,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_floatArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "floatArray_getitem" "', argument " "1"" of type '" "floatArray *""'"); } arg1 = (floatArray *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "floatArray_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (float)floatArray_getitem(arg1,arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_floatArray_setitem) { { floatArray *arg1 = (floatArray *) 0 ; size_t arg2 ; float arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; float val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: floatArray_setitem(self,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_floatArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "floatArray_setitem" "', argument " "1"" of type '" "floatArray *""'"); } arg1 = (floatArray *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "floatArray_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "floatArray_setitem" "', argument " "3"" of type '" "float""'"); } arg3 = (float)(val3); floatArray_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_floatArray_cast) { { floatArray *arg1 = (floatArray *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; float *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: floatArray_cast(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_floatArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "floatArray_cast" "', argument " "1"" of type '" "floatArray *""'"); } arg1 = (floatArray *)(argp1); result = (float *)floatArray_cast(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_float, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_floatArray_frompointer) { { float *arg1 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; floatArray *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: floatArray_frompointer(t);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "floatArray_frompointer" "', argument " "1"" of type '" "float *""'"); } arg1 = (float *)(argp1); result = (floatArray *)floatArray_frompointer(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_floatArray, 0 | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_doubleP) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; double *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_doubleP(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_doubleP" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (double *)new_doubleP(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_double, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_doubleP) { { double *arg1 = (double *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_doubleP(ary);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_doubleP" "', argument " "1"" of type '" "double *""'"); } arg1 = (double *)(argp1); delete_doubleP(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_doubleP_getitem) { { double *arg1 = (double *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: doubleP_getitem(ary,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "doubleP_getitem" "', argument " "1"" of type '" "double *""'"); } arg1 = (double *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "doubleP_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (double)doubleP_getitem(arg1,arg2); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_doubleP_setitem) { { double *arg1 = (double *) 0 ; size_t arg2 ; double arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; double val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: doubleP_setitem(ary,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "doubleP_setitem" "', argument " "1"" of type '" "double *""'"); } arg1 = (double *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "doubleP_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "doubleP_setitem" "', argument " "3"" of type '" "double""'"); } arg3 = (double)(val3); doubleP_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_doubleArray) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; doubleArray *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_doubleArray(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_doubleArray" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (doubleArray *)new_doubleArray(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_doubleArray, SWIG_OWNER | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_doubleArray) { { doubleArray *arg1 = (doubleArray *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_doubleArray(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_doubleArray, SWIG_POINTER_DISOWN | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_doubleArray" "', argument " "1"" of type '" "doubleArray *""'"); } arg1 = (doubleArray *)(argp1); delete_doubleArray(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_doubleArray_getitem) { { doubleArray *arg1 = (doubleArray *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: doubleArray_getitem(self,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_doubleArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "doubleArray_getitem" "', argument " "1"" of type '" "doubleArray *""'"); } arg1 = (doubleArray *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "doubleArray_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (double)doubleArray_getitem(arg1,arg2); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_doubleArray_setitem) { { doubleArray *arg1 = (doubleArray *) 0 ; size_t arg2 ; double arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; double val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: doubleArray_setitem(self,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_doubleArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "doubleArray_setitem" "', argument " "1"" of type '" "doubleArray *""'"); } arg1 = (doubleArray *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "doubleArray_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "doubleArray_setitem" "', argument " "3"" of type '" "double""'"); } arg3 = (double)(val3); doubleArray_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_doubleArray_cast) { { doubleArray *arg1 = (doubleArray *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; double *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: doubleArray_cast(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_doubleArray, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "doubleArray_cast" "', argument " "1"" of type '" "doubleArray *""'"); } arg1 = (doubleArray *)(argp1); result = (double *)doubleArray_cast(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_double, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_doubleArray_frompointer) { { double *arg1 = (double *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; doubleArray *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: doubleArray_frompointer(t);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "doubleArray_frompointer" "', argument " "1"" of type '" "double *""'"); } arg1 = (double *)(argp1); result = (doubleArray *)doubleArray_frompointer(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_doubleArray, 0 | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_ushortP) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; unsigned short *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_ushortP(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_ushortP" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (unsigned short *)new_ushortP(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_unsigned_short, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_ushortP) { { unsigned short *arg1 = (unsigned short *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_ushortP(ary);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_unsigned_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_ushortP" "', argument " "1"" of type '" "unsigned short *""'"); } arg1 = (unsigned short *)(argp1); delete_ushortP(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_ushortP_getitem) { { unsigned short *arg1 = (unsigned short *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; unsigned short result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: ushortP_getitem(ary,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_unsigned_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "ushortP_getitem" "', argument " "1"" of type '" "unsigned short *""'"); } arg1 = (unsigned short *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "ushortP_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (unsigned short)ushortP_getitem(arg1,arg2); ST(argvi) = SWIG_From_unsigned_SS_short SWIG_PERL_CALL_ARGS_1((unsigned short)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_ushortP_setitem) { { unsigned short *arg1 = (unsigned short *) 0 ; size_t arg2 ; unsigned short arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; unsigned short val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: ushortP_setitem(ary,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_unsigned_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "ushortP_setitem" "', argument " "1"" of type '" "unsigned short *""'"); } arg1 = (unsigned short *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "ushortP_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_unsigned_SS_short SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "ushortP_setitem" "', argument " "3"" of type '" "unsigned short""'"); } arg3 = (unsigned short)(val3); ushortP_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_shortP) { { size_t arg1 ; size_t val1 ; int ecode1 = 0 ; int argvi = 0; short *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: new_shortP(nelements);"); } ecode1 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_shortP" "', argument " "1"" of type '" "size_t""'"); } arg1 = (size_t)(val1); result = (short *)new_shortP(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_short, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_shortP) { { short *arg1 = (short *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_shortP(ary);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_shortP" "', argument " "1"" of type '" "short *""'"); } arg1 = (short *)(argp1); delete_shortP(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_shortP_getitem) { { short *arg1 = (short *) 0 ; size_t arg2 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; short result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: shortP_getitem(ary,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "shortP_getitem" "', argument " "1"" of type '" "short *""'"); } arg1 = (short *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "shortP_getitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); result = (short)shortP_getitem(arg1,arg2); ST(argvi) = SWIG_From_short SWIG_PERL_CALL_ARGS_1((short)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_shortP_setitem) { { short *arg1 = (short *) 0 ; size_t arg2 ; short arg3 ; void *argp1 = 0 ; int res1 = 0 ; size_t val2 ; int ecode2 = 0 ; short val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: shortP_setitem(ary,index,value);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "shortP_setitem" "', argument " "1"" of type '" "short *""'"); } arg1 = (short *)(argp1); ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "shortP_setitem" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); ecode3 = SWIG_AsVal_short SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "shortP_setitem" "', argument " "3"" of type '" "short""'"); } arg3 = (short)(val3); shortP_setitem(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_cdata) { { void *arg1 = (void *) 0 ; size_t arg2 = (size_t) 1 ; int res1 ; size_t val2 ; int ecode2 = 0 ; int argvi = 0; SWIGCDATA result; dXSARGS; if ((items < 1) || (items > 2)) { SWIG_croak("Usage: cdata(ptr,nelements);"); } res1 = SWIG_ConvertPtr(ST(0),SWIG_as_voidptrptr(&arg1), 0, 0); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "cdata" "', argument " "1"" of type '" "void *""'"); } if (items > 1) { ecode2 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "cdata" "', argument " "2"" of type '" "size_t""'"); } arg2 = (size_t)(val2); } result = cdata_void(arg1,arg2); ST(argvi) = SWIG_FromCharPtrAndSize((&result)->data,(&result)->len); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_memmove) { { void *arg1 = (void *) 0 ; void *arg2 = (void *) 0 ; size_t arg3 ; int res1 ; int res2 ; size_t val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: memmove(data,indata,inlen);"); } res1 = SWIG_ConvertPtr(ST(0),SWIG_as_voidptrptr(&arg1), 0, 0); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "memmove" "', argument " "1"" of type '" "void *""'"); } res2 = SWIG_ConvertPtr(ST(1),SWIG_as_voidptrptr(&arg2), 0, 0); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "memmove" "', argument " "2"" of type '" "void const *""'"); } ecode3 = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "memmove" "', argument " "3"" of type '" "size_t""'"); } arg3 = (size_t)(val3); memmove(arg1,(void const *)arg2,arg3); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_fold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) NULL ; float *arg3 = (float *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float temp3 ; int res3 = SWIG_TMPOBJ ; int argvi = 0; char *result = 0 ; dXSARGS; arg3 = &temp3; if ((items < 1) || (items > 2)) { SWIG_croak("Usage: fold(string,constraints);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "fold" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); if (items > 1) { res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "fold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); } result = (char *)my_fold(arg1,arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (SWIG_IsTmpObj(res3)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg3)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res3) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg3), SWIGTYPE_p_float, new_flags); argvi++ ; } if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_energy_of_structure) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: energy_of_structure(string,structure,verbosity_level);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "energy_of_structure" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_structure" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "energy_of_structure" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); result = (float)energy_of_structure((char const *)arg1,(char const *)arg2,arg3); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_energy_of_structure_pt) { { char *arg1 = (char *) 0 ; short *arg2 = (short *) 0 ; short *arg3 = (short *) 0 ; short *arg4 = (short *) 0 ; int arg5 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int val5 ; int ecode5 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 5) || (items > 5)) { SWIG_croak("Usage: energy_of_structure_pt(string,ptable,s,s1,verbosity_level);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "energy_of_structure_pt" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_structure_pt" "', argument " "2"" of type '" "short *""'"); } arg2 = (short *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "energy_of_structure_pt" "', argument " "3"" of type '" "short *""'"); } arg3 = (short *)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "energy_of_structure_pt" "', argument " "4"" of type '" "short *""'"); } arg4 = (short *)(argp4); ecode5 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(4), &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "energy_of_structure_pt" "', argument " "5"" of type '" "int""'"); } arg5 = (int)(val5); result = (int)energy_of_structure_pt((char const *)arg1,arg2,arg3,arg4,arg5); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_free_arrays) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: free_arrays();"); } free_arrays(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_parenthesis_structure) { { char *arg1 = (char *) 0 ; bondT *arg2 = (bondT *) 0 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: parenthesis_structure(structure,bp,length);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "parenthesis_structure" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_bondT, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "parenthesis_structure" "', argument " "2"" of type '" "bondT *""'"); } arg2 = (bondT *)(argp2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "parenthesis_structure" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); parenthesis_structure(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_parenthesis_zuker) { { char *arg1 = (char *) 0 ; bondT *arg2 = (bondT *) 0 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: parenthesis_zuker(structure,bp,length);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "parenthesis_zuker" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_bondT, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "parenthesis_zuker" "', argument " "2"" of type '" "bondT *""'"); } arg2 = (bondT *)(argp2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "parenthesis_zuker" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); parenthesis_zuker(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_letter_structure) { { char *arg1 = (char *) 0 ; bondT *arg2 = (bondT *) 0 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: letter_structure(structure,bp,length);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "letter_structure" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_bondT, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "letter_structure" "', argument " "2"" of type '" "bondT *""'"); } arg2 = (bondT *)(argp2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "letter_structure" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); letter_structure(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_update_fold_params) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: update_fold_params();"); } update_fold_params(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_backtrack_fold_from_pair) { { char *arg1 = (char *) 0 ; int arg2 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int val2 ; int ecode2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: backtrack_fold_from_pair(sequence,i,j);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "backtrack_fold_from_pair" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "backtrack_fold_from_pair" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "backtrack_fold_from_pair" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); result = (char *)backtrack_fold_from_pair(arg1,arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_loop_energy) { { short *arg1 = (short *) 0 ; short *arg2 = (short *) 0 ; short *arg3 = (short *) 0 ; int arg4 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; int val4 ; int ecode4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: loop_energy(ptable,s,s1,i);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "loop_energy" "', argument " "1"" of type '" "short *""'"); } arg1 = (short *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "loop_energy" "', argument " "2"" of type '" "short *""'"); } arg2 = (short *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "loop_energy" "', argument " "3"" of type '" "short *""'"); } arg3 = (short *)(argp3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "loop_energy" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); result = (int)loop_energy(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_export_fold_arrays) { { int **arg1 = (int **) 0 ; int **arg2 = (int **) 0 ; int **arg3 = (int **) 0 ; int **arg4 = (int **) 0 ; int **arg5 = (int **) 0 ; char **arg6 = (char **) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; void *argp5 = 0 ; int res5 = 0 ; int argvi = 0; dXSARGS; if ((items < 6) || (items > 6)) { SWIG_croak("Usage: export_fold_arrays(f5_p,c_p,fML_p,fM1_p,indx_p,ptype_p);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "export_fold_arrays" "', argument " "1"" of type '" "int **""'"); } arg1 = (int **)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "export_fold_arrays" "', argument " "2"" of type '" "int **""'"); } arg2 = (int **)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "export_fold_arrays" "', argument " "3"" of type '" "int **""'"); } arg3 = (int **)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "export_fold_arrays" "', argument " "4"" of type '" "int **""'"); } arg4 = (int **)(argp4); res5 = SWIG_ConvertPtr(ST(4), &argp5,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "export_fold_arrays" "', argument " "5"" of type '" "int **""'"); } arg5 = (int **)(argp5); { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(5))) croak("Argument 6 is not a reference."); if (SvTYPE(SvRV(ST(5))) != SVt_PVAV) croak("Argument 6 is not an array."); tempav = (AV*)SvRV(ST(5)); len = av_len(tempav); arg6 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg6[i] = (char *) SvPV(*tv,PL_na); } arg6[i] = NULL; } export_fold_arrays(arg1,arg2,arg3,arg4,arg5,arg6); ST(argvi) = sv_newmortal(); { free(arg6); } XSRETURN(argvi); fail: { free(arg6); } SWIG_croak_null(); } } XS(_wrap_circfold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: circfold(string,structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "circfold" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "circfold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); result = (float)circfold((char const *)arg1,arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_energy_of_circ_structure) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: energy_of_circ_structure(string,structure,verbosity_level);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "energy_of_circ_structure" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_circ_structure" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "energy_of_circ_structure" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); result = (float)energy_of_circ_structure((char const *)arg1,(char const *)arg2,arg3); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_export_circfold_arrays) { { int *arg1 = (int *) 0 ; int *arg2 = (int *) 0 ; int *arg3 = (int *) 0 ; int *arg4 = (int *) 0 ; int **arg5 = (int **) 0 ; int **arg6 = (int **) 0 ; int **arg7 = (int **) 0 ; int **arg8 = (int **) 0 ; int **arg9 = (int **) 0 ; int **arg10 = (int **) 0 ; char **arg11 = (char **) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; void *argp5 = 0 ; int res5 = 0 ; void *argp6 = 0 ; int res6 = 0 ; void *argp7 = 0 ; int res7 = 0 ; void *argp8 = 0 ; int res8 = 0 ; void *argp9 = 0 ; int res9 = 0 ; void *argp10 = 0 ; int res10 = 0 ; int argvi = 0; dXSARGS; if ((items < 11) || (items > 11)) { SWIG_croak("Usage: export_circfold_arrays(Fc_p,FcH_p,FcI_p,FcM_p,fM2_p,f5_p,c_p,fML_p,fM1_p,indx_p,ptype_p);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "export_circfold_arrays" "', argument " "1"" of type '" "int *""'"); } arg1 = (int *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "export_circfold_arrays" "', argument " "2"" of type '" "int *""'"); } arg2 = (int *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "export_circfold_arrays" "', argument " "3"" of type '" "int *""'"); } arg3 = (int *)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "export_circfold_arrays" "', argument " "4"" of type '" "int *""'"); } arg4 = (int *)(argp4); res5 = SWIG_ConvertPtr(ST(4), &argp5,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "export_circfold_arrays" "', argument " "5"" of type '" "int **""'"); } arg5 = (int **)(argp5); res6 = SWIG_ConvertPtr(ST(5), &argp6,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res6)) { SWIG_exception_fail(SWIG_ArgError(res6), "in method '" "export_circfold_arrays" "', argument " "6"" of type '" "int **""'"); } arg6 = (int **)(argp6); res7 = SWIG_ConvertPtr(ST(6), &argp7,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res7)) { SWIG_exception_fail(SWIG_ArgError(res7), "in method '" "export_circfold_arrays" "', argument " "7"" of type '" "int **""'"); } arg7 = (int **)(argp7); res8 = SWIG_ConvertPtr(ST(7), &argp8,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res8)) { SWIG_exception_fail(SWIG_ArgError(res8), "in method '" "export_circfold_arrays" "', argument " "8"" of type '" "int **""'"); } arg8 = (int **)(argp8); res9 = SWIG_ConvertPtr(ST(8), &argp9,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res9)) { SWIG_exception_fail(SWIG_ArgError(res9), "in method '" "export_circfold_arrays" "', argument " "9"" of type '" "int **""'"); } arg9 = (int **)(argp9); res10 = SWIG_ConvertPtr(ST(9), &argp10,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res10)) { SWIG_exception_fail(SWIG_ArgError(res10), "in method '" "export_circfold_arrays" "', argument " "10"" of type '" "int **""'"); } arg10 = (int **)(argp10); { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(10))) croak("Argument 11 is not a reference."); if (SvTYPE(SvRV(ST(10))) != SVt_PVAV) croak("Argument 11 is not an array."); tempav = (AV*)SvRV(ST(10)); len = av_len(tempav); arg11 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg11[i] = (char *) SvPV(*tv,PL_na); } arg11[i] = NULL; } export_circfold_arrays(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11); ST(argvi) = sv_newmortal(); { free(arg11); } XSRETURN(argvi); fail: { free(arg11); } SWIG_croak_null(); } } XS(_wrap_assign_plist_from_db) { { plist **arg1 = (plist **) 0 ; char *arg2 = (char *) 0 ; float arg3 ; void *argp1 = 0 ; int res1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: assign_plist_from_db(pl,struc,pr);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_plist, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "assign_plist_from_db" "', argument " "1"" of type '" "plist **""'"); } arg1 = (plist **)(argp1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "assign_plist_from_db" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "assign_plist_from_db" "', argument " "3"" of type '" "float""'"); } arg3 = (float)(val3); assign_plist_from_db(arg1,(char const *)arg2,arg3); ST(argvi) = sv_newmortal(); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_LoopEnergy) { { int arg1 ; int arg2 ; int arg3 ; int arg4 ; int arg5 ; int arg6 ; int arg7 ; int arg8 ; int val1 ; int ecode1 = 0 ; int val2 ; int ecode2 = 0 ; int val3 ; int ecode3 = 0 ; int val4 ; int ecode4 = 0 ; int val5 ; int ecode5 = 0 ; int val6 ; int ecode6 = 0 ; int val7 ; int ecode7 = 0 ; int val8 ; int ecode8 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 8) || (items > 8)) { SWIG_croak("Usage: LoopEnergy(n1,n2,type,type_2,si1,sj1,sp1,sq1);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "LoopEnergy" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "LoopEnergy" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "LoopEnergy" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "LoopEnergy" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); ecode5 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(4), &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "LoopEnergy" "', argument " "5"" of type '" "int""'"); } arg5 = (int)(val5); ecode6 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(5), &val6); if (!SWIG_IsOK(ecode6)) { SWIG_exception_fail(SWIG_ArgError(ecode6), "in method '" "LoopEnergy" "', argument " "6"" of type '" "int""'"); } arg6 = (int)(val6); ecode7 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(6), &val7); if (!SWIG_IsOK(ecode7)) { SWIG_exception_fail(SWIG_ArgError(ecode7), "in method '" "LoopEnergy" "', argument " "7"" of type '" "int""'"); } arg7 = (int)(val7); ecode8 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(7), &val8); if (!SWIG_IsOK(ecode8)) { SWIG_exception_fail(SWIG_ArgError(ecode8), "in method '" "LoopEnergy" "', argument " "8"" of type '" "int""'"); } arg8 = (int)(val8); result = (int)LoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_HairpinE) { { int arg1 ; int arg2 ; int arg3 ; int arg4 ; char *arg5 = (char *) 0 ; int val1 ; int ecode1 = 0 ; int val2 ; int ecode2 = 0 ; int val3 ; int ecode3 = 0 ; int val4 ; int ecode4 = 0 ; int res5 ; char *buf5 = 0 ; int alloc5 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 5) || (items > 5)) { SWIG_croak("Usage: HairpinE(size,type,si1,sj1,string);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "HairpinE" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "HairpinE" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "HairpinE" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "HairpinE" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); res5 = SWIG_AsCharPtrAndSize(ST(4), &buf5, NULL, &alloc5); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "HairpinE" "', argument " "5"" of type '" "char const *""'"); } arg5 = (char *)(buf5); result = (int)HairpinE(arg1,arg2,arg3,arg4,(char const *)arg5); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); XSRETURN(argvi); fail: if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); SWIG_croak_null(); } } XS(_wrap_initialize_fold) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: initialize_fold(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "initialize_fold" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); initialize_fold(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_energy_of_struct) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: energy_of_struct(string,structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "energy_of_struct" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_struct" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); result = (float)energy_of_struct((char const *)arg1,(char const *)arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_energy_of_struct_pt) { { char *arg1 = (char *) 0 ; short *arg2 = (short *) 0 ; short *arg3 = (short *) 0 ; short *arg4 = (short *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: energy_of_struct_pt(string,ptable,s,s1);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "energy_of_struct_pt" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_struct_pt" "', argument " "2"" of type '" "short *""'"); } arg2 = (short *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "energy_of_struct_pt" "', argument " "3"" of type '" "short *""'"); } arg3 = (short *)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "energy_of_struct_pt" "', argument " "4"" of type '" "short *""'"); } arg4 = (short *)(argp4); result = (int)energy_of_struct_pt((char const *)arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_energy_of_circ_struct) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: energy_of_circ_struct(string,structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "energy_of_circ_struct" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_circ_struct" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); result = (float)energy_of_circ_struct((char const *)arg1,(char const *)arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_cofold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) NULL ; float *arg3 = (float *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float temp3 ; int res3 = SWIG_TMPOBJ ; int argvi = 0; char *result = 0 ; dXSARGS; arg3 = &temp3; if ((items < 1) || (items > 2)) { SWIG_croak("Usage: cofold(string,constraints);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "cofold" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); if (items > 1) { res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "cofold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); } result = (char *)my_cofold(arg1,arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (SWIG_IsTmpObj(res3)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg3)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res3) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg3), SWIGTYPE_p_float, new_flags); argvi++ ; } if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_free_co_arrays) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: free_co_arrays();"); } free_co_arrays(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_update_cofold_params) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: update_cofold_params();"); } update_cofold_params(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_zukersubopt) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; SOLUTION *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: zukersubopt(string);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "zukersubopt" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); result = (SOLUTION *)zukersubopt((char const *)arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_SOLUTION, 0 | SWIG_SHADOW); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_get_monomere_mfes) { { float *arg1 = (float *) 0 ; float *arg2 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: get_monomere_mfes(e1,e2);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "get_monomere_mfes" "', argument " "1"" of type '" "float *""'"); } arg1 = (float *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "get_monomere_mfes" "', argument " "2"" of type '" "float *""'"); } arg2 = (float *)(argp2); get_monomere_mfes(arg1,arg2); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_export_cofold_arrays) { { int **arg1 = (int **) 0 ; int **arg2 = (int **) 0 ; int **arg3 = (int **) 0 ; int **arg4 = (int **) 0 ; int **arg5 = (int **) 0 ; int **arg6 = (int **) 0 ; char **arg7 = (char **) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; void *argp5 = 0 ; int res5 = 0 ; void *argp6 = 0 ; int res6 = 0 ; int argvi = 0; dXSARGS; if ((items < 7) || (items > 7)) { SWIG_croak("Usage: export_cofold_arrays(f5_p,c_p,fML_p,fM1_p,fc_p,indx_p,ptype_p);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "export_cofold_arrays" "', argument " "1"" of type '" "int **""'"); } arg1 = (int **)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "export_cofold_arrays" "', argument " "2"" of type '" "int **""'"); } arg2 = (int **)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "export_cofold_arrays" "', argument " "3"" of type '" "int **""'"); } arg3 = (int **)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "export_cofold_arrays" "', argument " "4"" of type '" "int **""'"); } arg4 = (int **)(argp4); res5 = SWIG_ConvertPtr(ST(4), &argp5,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "export_cofold_arrays" "', argument " "5"" of type '" "int **""'"); } arg5 = (int **)(argp5); res6 = SWIG_ConvertPtr(ST(5), &argp6,SWIGTYPE_p_p_int, 0 | 0 ); if (!SWIG_IsOK(res6)) { SWIG_exception_fail(SWIG_ArgError(res6), "in method '" "export_cofold_arrays" "', argument " "6"" of type '" "int **""'"); } arg6 = (int **)(argp6); { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(6))) croak("Argument 7 is not a reference."); if (SvTYPE(SvRV(ST(6))) != SVt_PVAV) croak("Argument 7 is not an array."); tempav = (AV*)SvRV(ST(6)); len = av_len(tempav); arg7 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg7[i] = (char *) SvPV(*tv,PL_na); } arg7[i] = NULL; } export_cofold_arrays(arg1,arg2,arg3,arg4,arg5,arg6,arg7); ST(argvi) = sv_newmortal(); { free(arg7); } XSRETURN(argvi); fail: { free(arg7); } SWIG_croak_null(); } } XS(_wrap_initialize_cofold) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: initialize_cofold(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "initialize_cofold" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); initialize_cofold(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_pf_fold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) NULL ; float *arg3 = (float *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float temp3 ; int res3 = SWIG_TMPOBJ ; int argvi = 0; char *result = 0 ; dXSARGS; arg3 = &temp3; if ((items < 1) || (items > 2)) { SWIG_croak("Usage: pf_fold(string,constraints);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "pf_fold" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); if (items > 1) { res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "pf_fold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); } result = (char *)my_pf_fold(arg1,arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (SWIG_IsTmpObj(res3)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg3)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res3) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg3), SWIGTYPE_p_float, new_flags); argvi++ ; } if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_pf_circ_fold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: pf_circ_fold(sequence,structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "pf_circ_fold" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "pf_circ_fold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); result = (float)pf_circ_fold((char const *)arg1,arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_pbacktrack) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: pbacktrack(sequence);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "pbacktrack" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)pbacktrack(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_pbacktrack_circ) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: pbacktrack_circ(sequence);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "pbacktrack_circ" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)pbacktrack_circ(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_free_pf_arrays) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: free_pf_arrays();"); } free_pf_arrays(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_update_pf_params) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: update_pf_params(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "update_pf_params" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); update_pf_params(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_export_bppm) { { int argvi = 0; double *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: export_bppm();"); } result = (double *)export_bppm(); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_double, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_assign_plist_from_pr) { { plist **arg1 = (plist **) 0 ; double *arg2 = (double *) 0 ; int arg3 ; double arg4 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int val3 ; int ecode3 = 0 ; double val4 ; int ecode4 = 0 ; int argvi = 0; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: assign_plist_from_pr(pl,probs,length,cutoff);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_plist, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "assign_plist_from_pr" "', argument " "1"" of type '" "plist **""'"); } arg1 = (plist **)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "assign_plist_from_pr" "', argument " "2"" of type '" "double *""'"); } arg2 = (double *)(argp2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "assign_plist_from_pr" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); ecode4 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "assign_plist_from_pr" "', argument " "4"" of type '" "double""'"); } arg4 = (double)(val4); assign_plist_from_pr(arg1,arg2,arg3,arg4); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_pf_arrays) { { short **arg1 = (short **) 0 ; short **arg2 = (short **) 0 ; char **arg3 = (char **) 0 ; double **arg4 = (double **) 0 ; double **arg5 = (double **) 0 ; double **arg6 = (double **) 0 ; double **arg7 = (double **) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp4 = 0 ; int res4 = 0 ; void *argp5 = 0 ; int res5 = 0 ; void *argp6 = 0 ; int res6 = 0 ; void *argp7 = 0 ; int res7 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 7) || (items > 7)) { SWIG_croak("Usage: get_pf_arrays(S_p,S1_p,ptype_p,qb_p,qm_p,q1k_p,qln_p);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "get_pf_arrays" "', argument " "1"" of type '" "short **""'"); } arg1 = (short **)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "get_pf_arrays" "', argument " "2"" of type '" "short **""'"); } arg2 = (short **)(argp2); { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(2))) croak("Argument 3 is not a reference."); if (SvTYPE(SvRV(ST(2))) != SVt_PVAV) croak("Argument 3 is not an array."); tempav = (AV*)SvRV(ST(2)); len = av_len(tempav); arg3 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg3[i] = (char *) SvPV(*tv,PL_na); } arg3[i] = NULL; } res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_p_double, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "get_pf_arrays" "', argument " "4"" of type '" "double **""'"); } arg4 = (double **)(argp4); res5 = SWIG_ConvertPtr(ST(4), &argp5,SWIGTYPE_p_p_double, 0 | 0 ); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "get_pf_arrays" "', argument " "5"" of type '" "double **""'"); } arg5 = (double **)(argp5); res6 = SWIG_ConvertPtr(ST(5), &argp6,SWIGTYPE_p_p_double, 0 | 0 ); if (!SWIG_IsOK(res6)) { SWIG_exception_fail(SWIG_ArgError(res6), "in method '" "get_pf_arrays" "', argument " "6"" of type '" "double **""'"); } arg6 = (double **)(argp6); res7 = SWIG_ConvertPtr(ST(6), &argp7,SWIGTYPE_p_p_double, 0 | 0 ); if (!SWIG_IsOK(res7)) { SWIG_exception_fail(SWIG_ArgError(res7), "in method '" "get_pf_arrays" "', argument " "7"" of type '" "double **""'"); } arg7 = (double **)(argp7); result = (int)get_pf_arrays(arg1,arg2,arg3,arg4,arg5,arg6,arg7); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; { free(arg3); } XSRETURN(argvi); fail: { free(arg3); } SWIG_croak_null(); } } XS(_wrap_get_centroid_struct_pl) { { int arg1 ; double *arg2 = (double *) 0 ; plist *arg3 = (plist *) 0 ; int val1 ; int ecode1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: get_centroid_struct_pl(length,dist,pl);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "get_centroid_struct_pl" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "get_centroid_struct_pl" "', argument " "2"" of type '" "double *""'"); } arg2 = (double *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_plist, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "get_centroid_struct_pl" "', argument " "3"" of type '" "plist *""'"); } arg3 = (plist *)(argp3); result = (char *)get_centroid_struct_pl(arg1,arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_centroid_struct_pr) { { int arg1 ; double *arg2 = (double *) 0 ; double *arg3 = (double *) 0 ; int val1 ; int ecode1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: get_centroid_struct_pr(length,dist,pr);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "get_centroid_struct_pr" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "get_centroid_struct_pr" "', argument " "2"" of type '" "double *""'"); } arg2 = (double *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "get_centroid_struct_pr" "', argument " "3"" of type '" "double *""'"); } arg3 = (double *)(argp3); result = (char *)get_centroid_struct_pr(arg1,arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_mean_bp_distance) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: mean_bp_distance(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "mean_bp_distance" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); result = (double)mean_bp_distance(arg1); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_mean_bp_distance_pr) { { int arg1 ; double *arg2 = (double *) 0 ; int val1 ; int ecode1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: mean_bp_distance_pr(length,pr);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "mean_bp_distance_pr" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "mean_bp_distance_pr" "', argument " "2"" of type '" "double *""'"); } arg2 = (double *)(argp2); result = (double)mean_bp_distance_pr(arg1,arg2); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_bppm_to_structure) { { char *arg1 = (char *) 0 ; double *arg2 = (double *) 0 ; unsigned int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; unsigned int val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: bppm_to_structure(structure,pr,length);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "bppm_to_structure" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "bppm_to_structure" "', argument " "2"" of type '" "double *""'"); } arg2 = (double *)(argp2); ecode3 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "bppm_to_structure" "', argument " "3"" of type '" "unsigned int""'"); } arg3 = (unsigned int)(val3); bppm_to_structure(arg1,arg2,arg3); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_stackProb) { { double arg1 ; double val1 ; int ecode1 = 0 ; int argvi = 0; plist *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: stackProb(cutoff);"); } ecode1 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "stackProb" "', argument " "1"" of type '" "double""'"); } arg1 = (double)(val1); result = (plist *)stackProb(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_plist, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_bppm_symbol) { { float *arg1 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; char result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: bppm_symbol(x);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "bppm_symbol" "', argument " "1"" of type '" "float const *""'"); } arg1 = (float *)(argp1); result = (char)bppm_symbol((float const *)arg1); ST(argvi) = SWIG_From_char SWIG_PERL_CALL_ARGS_1((char)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_init_pf_fold) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: init_pf_fold(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "init_pf_fold" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); init_pf_fold(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_centroid) { { int arg1 ; double *arg2 = (double *) 0 ; int val1 ; int ecode1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: centroid(length,dist);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "centroid" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "centroid" "', argument " "2"" of type '" "double *""'"); } arg2 = (double *)(argp2); result = (char *)centroid(arg1,arg2); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_mean_bp_dist) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: mean_bp_dist(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "mean_bp_dist" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); result = (double)mean_bp_dist(arg1); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_expLoopEnergy) { { int arg1 ; int arg2 ; int arg3 ; int arg4 ; short arg5 ; short arg6 ; short arg7 ; short arg8 ; int val1 ; int ecode1 = 0 ; int val2 ; int ecode2 = 0 ; int val3 ; int ecode3 = 0 ; int val4 ; int ecode4 = 0 ; short val5 ; int ecode5 = 0 ; short val6 ; int ecode6 = 0 ; short val7 ; int ecode7 = 0 ; short val8 ; int ecode8 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 8) || (items > 8)) { SWIG_croak("Usage: expLoopEnergy(u1,u2,type,type2,si1,sj1,sp1,sq1);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "expLoopEnergy" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "expLoopEnergy" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "expLoopEnergy" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "expLoopEnergy" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); ecode5 = SWIG_AsVal_short SWIG_PERL_CALL_ARGS_2(ST(4), &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "expLoopEnergy" "', argument " "5"" of type '" "short""'"); } arg5 = (short)(val5); ecode6 = SWIG_AsVal_short SWIG_PERL_CALL_ARGS_2(ST(5), &val6); if (!SWIG_IsOK(ecode6)) { SWIG_exception_fail(SWIG_ArgError(ecode6), "in method '" "expLoopEnergy" "', argument " "6"" of type '" "short""'"); } arg6 = (short)(val6); ecode7 = SWIG_AsVal_short SWIG_PERL_CALL_ARGS_2(ST(6), &val7); if (!SWIG_IsOK(ecode7)) { SWIG_exception_fail(SWIG_ArgError(ecode7), "in method '" "expLoopEnergy" "', argument " "7"" of type '" "short""'"); } arg7 = (short)(val7); ecode8 = SWIG_AsVal_short SWIG_PERL_CALL_ARGS_2(ST(7), &val8); if (!SWIG_IsOK(ecode8)) { SWIG_exception_fail(SWIG_ArgError(ecode8), "in method '" "expLoopEnergy" "', argument " "8"" of type '" "short""'"); } arg8 = (short)(val8); result = (double)expLoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_expHairpinEnergy) { { int arg1 ; int arg2 ; short arg3 ; short arg4 ; char *arg5 = (char *) 0 ; int val1 ; int ecode1 = 0 ; int val2 ; int ecode2 = 0 ; short val3 ; int ecode3 = 0 ; short val4 ; int ecode4 = 0 ; int res5 ; char *buf5 = 0 ; int alloc5 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 5) || (items > 5)) { SWIG_croak("Usage: expHairpinEnergy(u,type,si1,sj1,string);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "expHairpinEnergy" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "expHairpinEnergy" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); ecode3 = SWIG_AsVal_short SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "expHairpinEnergy" "', argument " "3"" of type '" "short""'"); } arg3 = (short)(val3); ecode4 = SWIG_AsVal_short SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "expHairpinEnergy" "', argument " "4"" of type '" "short""'"); } arg4 = (short)(val4); res5 = SWIG_AsCharPtrAndSize(ST(4), &buf5, NULL, &alloc5); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "expHairpinEnergy" "', argument " "5"" of type '" "char const *""'"); } arg5 = (char *)(buf5); result = (double)expHairpinEnergy(arg1,arg2,arg3,arg4,(char const *)arg5); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); XSRETURN(argvi); fail: if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); SWIG_croak_null(); } } XS(_wrap_co_pf_fold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) NULL ; float *arg3 = (float *) 0 ; float *arg4 = (float *) 0 ; float *arg5 = (float *) 0 ; float *arg6 = (float *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float temp3 ; int res3 = SWIG_TMPOBJ ; float temp4 ; int res4 = SWIG_TMPOBJ ; float temp5 ; int res5 = SWIG_TMPOBJ ; float temp6 ; int res6 = SWIG_TMPOBJ ; int argvi = 0; char *result = 0 ; dXSARGS; arg3 = &temp3; arg4 = &temp4; arg5 = &temp5; arg6 = &temp6; if ((items < 1) || (items > 2)) { SWIG_croak("Usage: co_pf_fold(string,constraints);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "co_pf_fold" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); if (items > 1) { res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "co_pf_fold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); } result = (char *)my_co_pf_fold(arg1,arg2,arg3,arg4,arg5,arg6); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (SWIG_IsTmpObj(res3)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg3)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res3) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg3), SWIGTYPE_p_float, new_flags); argvi++ ; } if (SWIG_IsTmpObj(res4)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg4)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res4) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg4), SWIGTYPE_p_float, new_flags); argvi++ ; } if (SWIG_IsTmpObj(res5)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg5)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res5) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg5), SWIGTYPE_p_float, new_flags); argvi++ ; } if (SWIG_IsTmpObj(res6)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg6)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res6) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg6), SWIGTYPE_p_float, new_flags); argvi++ ; } if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_free_co_pf_arrays) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: free_co_pf_arrays();"); } free_co_pf_arrays(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_update_co_pf_params) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: update_co_pf_params(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "update_co_pf_params" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); update_co_pf_params(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_concentrations__SWIG_0) { { double arg1 ; double arg2 ; double arg3 ; double arg4 ; double arg5 ; double *arg6 = (double *) 0 ; double val1 ; int ecode1 = 0 ; double val2 ; int ecode2 = 0 ; double val3 ; int ecode3 = 0 ; double val4 ; int ecode4 = 0 ; double val5 ; int ecode5 = 0 ; void *argp6 = 0 ; int res6 = 0 ; int argvi = 0; ConcEnt *result = 0 ; dXSARGS; if ((items < 6) || (items > 6)) { SWIG_croak("Usage: get_concentrations(FEAB,FEAA,FEBB,FEA,FEB,startconc);"); } ecode1 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "get_concentrations" "', argument " "1"" of type '" "double""'"); } arg1 = (double)(val1); ecode2 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "get_concentrations" "', argument " "2"" of type '" "double""'"); } arg2 = (double)(val2); ecode3 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "get_concentrations" "', argument " "3"" of type '" "double""'"); } arg3 = (double)(val3); ecode4 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "get_concentrations" "', argument " "4"" of type '" "double""'"); } arg4 = (double)(val4); ecode5 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(4), &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "get_concentrations" "', argument " "5"" of type '" "double""'"); } arg5 = (double)(val5); res6 = SWIG_ConvertPtr(ST(5), &argp6,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res6)) { SWIG_exception_fail(SWIG_ArgError(res6), "in method '" "get_concentrations" "', argument " "6"" of type '" "double *""'"); } arg6 = (double *)(argp6); result = (ConcEnt *)get_concentrations(arg1,arg2,arg3,arg4,arg5,arg6); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_ConcEnt, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_concentrations__SWIG_1) { { double arg1 ; double arg2 ; double arg3 ; double arg4 ; double arg5 ; double arg6 ; double arg7 ; double *arg8 = (double *) 0 ; double *arg9 = (double *) 0 ; double *arg10 = (double *) 0 ; double *arg11 = (double *) 0 ; double *arg12 = (double *) 0 ; double val1 ; int ecode1 = 0 ; double val2 ; int ecode2 = 0 ; double val3 ; int ecode3 = 0 ; double val4 ; int ecode4 = 0 ; double val5 ; int ecode5 = 0 ; double val6 ; int ecode6 = 0 ; double val7 ; int ecode7 = 0 ; double temp8 ; int res8 = SWIG_TMPOBJ ; double temp9 ; int res9 = SWIG_TMPOBJ ; double temp10 ; int res10 = SWIG_TMPOBJ ; double temp11 ; int res11 = SWIG_TMPOBJ ; double temp12 ; int res12 = SWIG_TMPOBJ ; int argvi = 0; dXSARGS; arg8 = &temp8; arg9 = &temp9; arg10 = &temp10; arg11 = &temp11; arg12 = &temp12; if ((items < 7) || (items > 7)) { SWIG_croak("Usage: get_concentrations(FcAB,FcAA,FcBB,FEA,FEB,A0,BO);"); } ecode1 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "get_concentrations" "', argument " "1"" of type '" "double""'"); } arg1 = (double)(val1); ecode2 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "get_concentrations" "', argument " "2"" of type '" "double""'"); } arg2 = (double)(val2); ecode3 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "get_concentrations" "', argument " "3"" of type '" "double""'"); } arg3 = (double)(val3); ecode4 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "get_concentrations" "', argument " "4"" of type '" "double""'"); } arg4 = (double)(val4); ecode5 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(4), &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "get_concentrations" "', argument " "5"" of type '" "double""'"); } arg5 = (double)(val5); ecode6 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(5), &val6); if (!SWIG_IsOK(ecode6)) { SWIG_exception_fail(SWIG_ArgError(ecode6), "in method '" "get_concentrations" "', argument " "6"" of type '" "double""'"); } arg6 = (double)(val6); ecode7 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(6), &val7); if (!SWIG_IsOK(ecode7)) { SWIG_exception_fail(SWIG_ArgError(ecode7), "in method '" "get_concentrations" "', argument " "7"" of type '" "double""'"); } arg7 = (double)(val7); my_get_concentrations(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12); ST(argvi) = sv_newmortal(); if (SWIG_IsTmpObj(res8)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((*arg8)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res8) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg8), SWIGTYPE_p_double, new_flags); argvi++ ; } if (SWIG_IsTmpObj(res9)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((*arg9)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res9) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg9), SWIGTYPE_p_double, new_flags); argvi++ ; } if (SWIG_IsTmpObj(res10)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((*arg10)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res10) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg10), SWIGTYPE_p_double, new_flags); argvi++ ; } if (SWIG_IsTmpObj(res11)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((*arg11)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res11) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg11), SWIGTYPE_p_double, new_flags); argvi++ ; } if (SWIG_IsTmpObj(res12)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((*arg12)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res12) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg12), SWIGTYPE_p_double, new_flags); argvi++ ; } XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_concentrations) { dXSARGS; { unsigned long _index = 0; SWIG_TypeRank _rank = 0; if (items == 6) { SWIG_TypeRank _ranki = 0; SWIG_TypeRank _rankm = 0; SWIG_TypeRank _pi = 1; int _v = 0; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(0), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_1; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(1), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_1; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double 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; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(3), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_1; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(4), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_1; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { void *vptr = 0; int res = SWIG_ConvertPtr(ST(5), &vptr, SWIGTYPE_p_double, 0); _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 == 7) { SWIG_TypeRank _ranki = 0; SWIG_TypeRank _rankm = 0; SWIG_TypeRank _pi = 1; int _v = 0; { { int res = SWIG_AsVal_double 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; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(1), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_2; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(2), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_2; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(3), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_2; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(4), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_2; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(5), NULL); _v = SWIG_CheckState(res); } } if (!_v) goto check_2; _ranki += _v*_pi; _rankm += _pi; _pi *= SWIG_MAXCASTRANK; { { int res = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(6), 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: dispatch: switch(_index) { case 1: ++PL_markstack_ptr; SWIG_CALLXS(_wrap_get_concentrations__SWIG_0); return; case 2: ++PL_markstack_ptr; SWIG_CALLXS(_wrap_get_concentrations__SWIG_1); return; } } croak("No matching function for overloaded 'get_concentrations'"); XSRETURN(0); } XS(_wrap_inverse_fold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; float *arg3 = (float *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float temp3 ; int res3 = SWIG_TMPOBJ ; int argvi = 0; char *result = 0 ; dXSARGS; arg3 = &temp3; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: inverse_fold(start,target);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "inverse_fold" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "inverse_fold" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); result = (char *)my_inverse_fold(arg1,(char const *)arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (SWIG_IsTmpObj(res3)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg3)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res3) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg3), SWIGTYPE_p_float, new_flags); argvi++ ; } if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_inverse_pf_fold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; float *arg3 = (float *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float temp3 ; int res3 = SWIG_TMPOBJ ; int argvi = 0; char *result = 0 ; dXSARGS; arg3 = &temp3; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: inverse_pf_fold(start,target);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "inverse_pf_fold" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "inverse_pf_fold" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); result = (char *)my_inverse_pf_fold(arg1,(char const *)arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (SWIG_IsTmpObj(res3)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg3)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res3) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg3), SWIGTYPE_p_float, new_flags); argvi++ ; } if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_option_string) { { int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: option_string();"); } result = (char *)option_string(); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_update_alifold_params) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: update_alifold_params();"); } update_alifold_params(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_circalifold) { { char **arg1 = (char **) 0 ; char *arg2 = (char *) 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: circalifold(strings,structure);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "circalifold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); result = (float)circalifold((char const **)arg1,arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_free_alifold_arrays) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: free_alifold_arrays();"); } free_alifold_arrays(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_mpi) { { char **arg1 ; int arg2 ; int arg3 ; int *arg4 = (int *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int val2 ; int ecode2 = 0 ; int val3 ; int ecode3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: get_mpi(Alseq,n_seq,length,mini);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_char, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "get_mpi" "', argument " "1"" of type '" "char *[]""'"); } arg1 = (char **)(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 '" "get_mpi" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "get_mpi" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "get_mpi" "', argument " "4"" of type '" "int *""'"); } arg4 = (int *)(argp4); result = (int)get_mpi(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_readribosum) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; float **result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: readribosum(name);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "readribosum" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (float **)readribosum(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_p_float, 0 | 0); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_energy_of_alistruct) { { char **arg1 = (char **) 0 ; char *arg2 = (char *) 0 ; int arg3 ; float *arg4 = (float *) 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: energy_of_alistruct(sequences,structure,n_seq,energy);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_alistruct" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "energy_of_alistruct" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "energy_of_alistruct" "', argument " "4"" of type '" "float *""'"); } arg4 = (float *)(argp4); result = (float)energy_of_alistruct((char const **)arg1,(char const *)arg2,arg3,arg4); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_encode_ali_sequence) { { char *arg1 = (char *) 0 ; short *arg2 = (short *) 0 ; short *arg3 = (short *) 0 ; short *arg4 = (short *) 0 ; char *arg5 = (char *) 0 ; unsigned short *arg6 = (unsigned short *) 0 ; int arg7 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int res5 ; char *buf5 = 0 ; int alloc5 = 0 ; void *argp6 = 0 ; int res6 = 0 ; int val7 ; int ecode7 = 0 ; int argvi = 0; dXSARGS; if ((items < 7) || (items > 7)) { SWIG_croak("Usage: encode_ali_sequence(sequence,S,s5,s3,ss,as,circ);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "encode_ali_sequence" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "encode_ali_sequence" "', argument " "2"" of type '" "short *""'"); } arg2 = (short *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "encode_ali_sequence" "', argument " "3"" of type '" "short *""'"); } arg3 = (short *)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "encode_ali_sequence" "', argument " "4"" of type '" "short *""'"); } arg4 = (short *)(argp4); res5 = SWIG_AsCharPtrAndSize(ST(4), &buf5, NULL, &alloc5); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "encode_ali_sequence" "', argument " "5"" of type '" "char *""'"); } arg5 = (char *)(buf5); res6 = SWIG_ConvertPtr(ST(5), &argp6,SWIGTYPE_p_unsigned_short, 0 | 0 ); if (!SWIG_IsOK(res6)) { SWIG_exception_fail(SWIG_ArgError(res6), "in method '" "encode_ali_sequence" "', argument " "6"" of type '" "unsigned short *""'"); } arg6 = (unsigned short *)(argp6); ecode7 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(6), &val7); if (!SWIG_IsOK(ecode7)) { SWIG_exception_fail(SWIG_ArgError(ecode7), "in method '" "encode_ali_sequence" "', argument " "7"" of type '" "int""'"); } arg7 = (int)(val7); encode_ali_sequence((char const *)arg1,arg2,arg3,arg4,arg5,arg6,arg7); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); SWIG_croak_null(); } } XS(_wrap_alloc_sequence_arrays) { { char **arg1 = (char **) 0 ; short ***arg2 = (short ***) 0 ; short ***arg3 = (short ***) 0 ; short ***arg4 = (short ***) 0 ; unsigned short ***arg5 = (unsigned short ***) 0 ; char ***arg6 = (char ***) 0 ; int arg7 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; void *argp5 = 0 ; int res5 = 0 ; void *argp6 = 0 ; int res6 = 0 ; int val7 ; int ecode7 = 0 ; int argvi = 0; dXSARGS; if ((items < 7) || (items > 7)) { SWIG_croak("Usage: alloc_sequence_arrays(sequences,S,S5,S3,a2s,Ss,circ);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "alloc_sequence_arrays" "', argument " "2"" of type '" "short ***""'"); } arg2 = (short ***)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "alloc_sequence_arrays" "', argument " "3"" of type '" "short ***""'"); } arg3 = (short ***)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "alloc_sequence_arrays" "', argument " "4"" of type '" "short ***""'"); } arg4 = (short ***)(argp4); res5 = SWIG_ConvertPtr(ST(4), &argp5,SWIGTYPE_p_p_p_unsigned_short, 0 | 0 ); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "alloc_sequence_arrays" "', argument " "5"" of type '" "unsigned short ***""'"); } arg5 = (unsigned short ***)(argp5); res6 = SWIG_ConvertPtr(ST(5), &argp6,SWIGTYPE_p_p_p_char, 0 | 0 ); if (!SWIG_IsOK(res6)) { SWIG_exception_fail(SWIG_ArgError(res6), "in method '" "alloc_sequence_arrays" "', argument " "6"" of type '" "char ***""'"); } arg6 = (char ***)(argp6); ecode7 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(6), &val7); if (!SWIG_IsOK(ecode7)) { SWIG_exception_fail(SWIG_ArgError(ecode7), "in method '" "alloc_sequence_arrays" "', argument " "7"" of type '" "int""'"); } arg7 = (int)(val7); alloc_sequence_arrays((char const **)arg1,arg2,arg3,arg4,arg5,arg6,arg7); ST(argvi) = sv_newmortal(); { free(arg1); } XSRETURN(argvi); fail: { free(arg1); } SWIG_croak_null(); } } XS(_wrap_free_sequence_arrays) { { unsigned int arg1 ; short ***arg2 = (short ***) 0 ; short ***arg3 = (short ***) 0 ; short ***arg4 = (short ***) 0 ; unsigned short ***arg5 = (unsigned short ***) 0 ; char ***arg6 = (char ***) 0 ; unsigned int val1 ; int ecode1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; void *argp5 = 0 ; int res5 = 0 ; void *argp6 = 0 ; int res6 = 0 ; int argvi = 0; dXSARGS; if ((items < 6) || (items > 6)) { SWIG_croak("Usage: free_sequence_arrays(n_seq,S,S5,S3,a2s,Ss);"); } 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 '" "free_sequence_arrays" "', argument " "1"" of type '" "unsigned int""'"); } arg1 = (unsigned int)(val1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "free_sequence_arrays" "', argument " "2"" of type '" "short ***""'"); } arg2 = (short ***)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "free_sequence_arrays" "', argument " "3"" of type '" "short ***""'"); } arg3 = (short ***)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_p_p_short, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "free_sequence_arrays" "', argument " "4"" of type '" "short ***""'"); } arg4 = (short ***)(argp4); res5 = SWIG_ConvertPtr(ST(4), &argp5,SWIGTYPE_p_p_p_unsigned_short, 0 | 0 ); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "free_sequence_arrays" "', argument " "5"" of type '" "unsigned short ***""'"); } arg5 = (unsigned short ***)(argp5); res6 = SWIG_ConvertPtr(ST(5), &argp6,SWIGTYPE_p_p_p_char, 0 | 0 ); if (!SWIG_IsOK(res6)) { SWIG_exception_fail(SWIG_ArgError(res6), "in method '" "free_sequence_arrays" "', argument " "6"" of type '" "char ***""'"); } arg6 = (char ***)(argp6); free_sequence_arrays(arg1,arg2,arg3,arg4,arg5,arg6); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_alipf_fold) { { char **arg1 = (char **) 0 ; char *arg2 = (char *) 0 ; plist **arg3 = (plist **) 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: alipf_fold(sequences,structure,pl);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "alipf_fold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_plist, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "alipf_fold" "', argument " "3"" of type '" "plist **""'"); } arg3 = (plist **)(argp3); result = (float)alipf_fold((char const **)arg1,arg2,arg3); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_alipf_circ_fold) { { char **arg1 = (char **) 0 ; char *arg2 = (char *) 0 ; plist **arg3 = (plist **) 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: alipf_circ_fold(sequences,structure,pl);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "alipf_circ_fold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_plist, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "alipf_circ_fold" "', argument " "3"" of type '" "plist **""'"); } arg3 = (plist **)(argp3); result = (float)alipf_circ_fold((char const **)arg1,arg2,arg3); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_free_alipf_arrays) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: free_alipf_arrays();"); } free_alipf_arrays(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_alipbacktrack) { { double *arg1 = (double *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: alipbacktrack(prob);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "alipbacktrack" "', argument " "1"" of type '" "double *""'"); } arg1 = (double *)(argp1); result = (char *)alipbacktrack(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_alifold) { { char **arg1 = (char **) 0 ; char *arg2 = (char *) NULL ; float *arg3 = (float *) 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; float temp3 ; int res3 = SWIG_TMPOBJ ; int argvi = 0; char *result = 0 ; dXSARGS; arg3 = &temp3; if ((items < 1) || (items > 2)) { SWIG_croak("Usage: alifold(strings,constraints);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } if (items > 1) { res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "alifold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); } result = (char *)my_alifold(arg1,arg2,arg3); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (SWIG_IsTmpObj(res3)) { if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((*arg3)); argvi++ ; } else { int new_flags = SWIG_IsNewObj(res3) ? (SWIG_POINTER_OWN | 0) : 0; if (argvi >= items) EXTEND(sp,1); ST(argvi) = SWIG_NewPointerObj((void*)(arg3), SWIGTYPE_p_float, new_flags); argvi++ ; } { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_consensus) { { char **arg1 = (char **) 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: consensus(AS);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } result = (char *)consensus((char const **)arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; { free(arg1); } free((char*)result); XSRETURN(argvi); fail: { free(arg1); } SWIG_croak_null(); } } XS(_wrap_consens_mis) { { char **arg1 = (char **) 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: consens_mis(AS);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } result = (char *)consens_mis((char const **)arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; { free(arg1); } XSRETURN(argvi); fail: { free(arg1); } SWIG_croak_null(); } } XS(_wrap_COORDINATE_X_set) { { COORDINATE *arg1 = (COORDINATE *) 0 ; float arg2 ; void *argp1 = 0 ; int res1 = 0 ; float val2 ; int ecode2 = 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: COORDINATE_X_set(self,X);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_COORDINATE, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "COORDINATE_X_set" "', argument " "1"" of type '" "COORDINATE *""'"); } arg1 = (COORDINATE *)(argp1); ecode2 = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "COORDINATE_X_set" "', argument " "2"" of type '" "float""'"); } arg2 = (float)(val2); if (arg1) (arg1)->X = arg2; ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_COORDINATE_X_get) { { COORDINATE *arg1 = (COORDINATE *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: COORDINATE_X_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_COORDINATE, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "COORDINATE_X_get" "', argument " "1"" of type '" "COORDINATE *""'"); } arg1 = (COORDINATE *)(argp1); result = (float) ((arg1)->X); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_COORDINATE_Y_set) { { COORDINATE *arg1 = (COORDINATE *) 0 ; float arg2 ; void *argp1 = 0 ; int res1 = 0 ; float val2 ; int ecode2 = 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: COORDINATE_Y_set(self,Y);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_COORDINATE, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "COORDINATE_Y_set" "', argument " "1"" of type '" "COORDINATE *""'"); } arg1 = (COORDINATE *)(argp1); ecode2 = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "COORDINATE_Y_set" "', argument " "2"" of type '" "float""'"); } arg2 = (float)(val2); if (arg1) (arg1)->Y = arg2; ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_COORDINATE_Y_get) { { COORDINATE *arg1 = (COORDINATE *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: COORDINATE_Y_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_COORDINATE, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "COORDINATE_Y_get" "', argument " "1"" of type '" "COORDINATE *""'"); } arg1 = (COORDINATE *)(argp1); result = (float) ((arg1)->Y); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_COORDINATE_get) { { COORDINATE *arg1 = (COORDINATE *) 0 ; int arg2 ; void *argp1 = 0 ; int res1 = 0 ; int val2 ; int ecode2 = 0 ; int argvi = 0; COORDINATE *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: COORDINATE_get(self,i);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_COORDINATE, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "COORDINATE_get" "', argument " "1"" of type '" "COORDINATE *""'"); } arg1 = (COORDINATE *)(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 '" "COORDINATE_get" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); result = (COORDINATE *)COORDINATE_get(arg1,arg2); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_COORDINATE, 0 | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_COORDINATE) { { int argvi = 0; COORDINATE *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: new_COORDINATE();"); } result = (COORDINATE *)calloc(1, sizeof(COORDINATE)); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_COORDINATE, SWIG_OWNER | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_COORDINATE) { { COORDINATE *arg1 = (COORDINATE *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_COORDINATE(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_COORDINATE, SWIG_POINTER_DISOWN | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_COORDINATE" "', argument " "1"" of type '" "COORDINATE *""'"); } arg1 = (COORDINATE *)(argp1); free((char *) arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_xy_coordinates) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; COORDINATE *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: get_xy_coordinates(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "get_xy_coordinates" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); result = (COORDINATE *)get_xy_coordinates((char const *)arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_COORDINATE, 0 | SWIG_SHADOW); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_SOLUTION_energy_set) { { SOLUTION *arg1 = (SOLUTION *) 0 ; float arg2 ; void *argp1 = 0 ; int res1 = 0 ; float val2 ; int ecode2 = 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: SOLUTION_energy_set(self,energy);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_SOLUTION, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SOLUTION_energy_set" "', argument " "1"" of type '" "SOLUTION *""'"); } arg1 = (SOLUTION *)(argp1); ecode2 = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "SOLUTION_energy_set" "', argument " "2"" of type '" "float""'"); } arg2 = (float)(val2); if (arg1) (arg1)->energy = arg2; ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_SOLUTION_energy_get) { { SOLUTION *arg1 = (SOLUTION *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: SOLUTION_energy_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_SOLUTION, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SOLUTION_energy_get" "', argument " "1"" of type '" "SOLUTION *""'"); } arg1 = (SOLUTION *)(argp1); result = (float) ((arg1)->energy); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_SOLUTION_structure_set) { { SOLUTION *arg1 = (SOLUTION *) 0 ; char *arg2 = (char *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: SOLUTION_structure_set(self,structure);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_SOLUTION, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SOLUTION_structure_set" "', argument " "1"" of type '" "SOLUTION *""'"); } arg1 = (SOLUTION *)(argp1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "SOLUTION_structure_set" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); if (arg1->structure) free((char*)arg1->structure); if (arg2) { size_t size = strlen((const char *)(arg2)) + 1; arg1->structure = (char *)(char *)memcpy((char *)malloc((size)*sizeof(char)), (const char *)(arg2), sizeof(char)*(size)); } else { arg1->structure = 0; } ST(argvi) = sv_newmortal(); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_SOLUTION_structure_get) { { SOLUTION *arg1 = (SOLUTION *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: SOLUTION_structure_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_SOLUTION, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SOLUTION_structure_get" "', argument " "1"" of type '" "SOLUTION *""'"); } arg1 = (SOLUTION *)(argp1); result = (char *) ((arg1)->structure); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_SOLUTION_get) { { SOLUTION *arg1 = (SOLUTION *) 0 ; int arg2 ; void *argp1 = 0 ; int res1 = 0 ; int val2 ; int ecode2 = 0 ; int argvi = 0; SOLUTION *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: SOLUTION_get(self,i);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_SOLUTION, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SOLUTION_get" "', argument " "1"" of type '" "SOLUTION *""'"); } arg1 = (SOLUTION *)(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 '" "SOLUTION_get" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); result = (SOLUTION *)SOLUTION_get(arg1,arg2); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_SOLUTION, 0 | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_SOLUTION_size) { { SOLUTION *arg1 = (SOLUTION *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: SOLUTION_size(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_SOLUTION, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SOLUTION_size" "', argument " "1"" of type '" "SOLUTION *""'"); } arg1 = (SOLUTION *)(argp1); result = (int)SOLUTION_size(arg1); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_SOLUTION) { { SOLUTION *arg1 = (SOLUTION *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_SOLUTION(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_SOLUTION, SWIG_POINTER_DISOWN | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_SOLUTION" "', argument " "1"" of type '" "SOLUTION *""'"); } arg1 = (SOLUTION *)(argp1); delete_SOLUTION(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_SOLUTION) { { int argvi = 0; SOLUTION *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: new_SOLUTION();"); } result = (SOLUTION *)calloc(1, sizeof(SOLUTION)); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_SOLUTION, SWIG_OWNER | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_subopt) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int arg3 ; FILE *arg4 = (FILE *) NULL ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; SOLUTION *result = 0 ; dXSARGS; if ((items < 3) || (items > 4)) { SWIG_croak("Usage: subopt(seq,constraint,delta,fp);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "subopt" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "subopt" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "subopt" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); if (items > 3) { { if (SvOK(ST(3))) /* check for undef */ arg4 = PerlIO_findFILE(IoIFP(sv_2io(ST(3)))); else arg4 = NULL; } } result = (SOLUTION *)subopt(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_SOLUTION, SWIG_OWNER | SWIG_SHADOW); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_get_pr) { { int arg1 ; int arg2 ; int val1 ; int ecode1 = 0 ; int val2 ; int ecode2 = 0 ; int argvi = 0; double result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: get_pr(i,j);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "get_pr" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "get_pr" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); result = (double)get_pr(arg1,arg2); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_b2HIT) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: b2HIT(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "b2HIT" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)b2HIT(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_b2C) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: b2C(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "b2C" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)b2C(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_b2Shapiro) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: b2Shapiro(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "b2Shapiro" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)b2Shapiro(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_add_root) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: add_root(char *);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "add_root" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)add_root(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_expand_Shapiro) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: expand_Shapiro(coarse);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "expand_Shapiro" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)expand_Shapiro(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_expand_Full) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: expand_Full(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "expand_Full" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)expand_Full(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_unexpand_Full) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: unexpand_Full(ffull);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "unexpand_Full" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)unexpand_Full(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_unweight) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: unweight(wcoarse);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "unweight" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (char *)unweight(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_unexpand_aligned_F) { { char **arg1 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: unexpand_aligned_F(align);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_char, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "unexpand_aligned_F" "', argument " "1"" of type '" "char *[2]""'"); } arg1 = (char **)(argp1); unexpand_aligned_F(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_parse_structure) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: parse_structure(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "parse_structure" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); parse_structure(arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_make_tree) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; Tree *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: make_tree(struc);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "make_tree" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (Tree *)make_tree(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_Tree, 0 | 0); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_tree_edit_distance) { { Tree *arg1 = (Tree *) 0 ; Tree *arg2 = (Tree *) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: tree_edit_distance(T1,T2);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_Tree, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "tree_edit_distance" "', argument " "1"" of type '" "Tree *""'"); } arg1 = (Tree *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_Tree, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "tree_edit_distance" "', argument " "2"" of type '" "Tree *""'"); } arg2 = (Tree *)(argp2); result = (float)tree_edit_distance(arg1,arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_print_tree) { { Tree *arg1 = (Tree *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: print_tree(t);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_Tree, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "print_tree" "', argument " "1"" of type '" "Tree *""'"); } arg1 = (Tree *)(argp1); print_tree(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_free_tree) { { Tree *arg1 = (Tree *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: free_tree(t);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_Tree, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "free_tree" "', argument " "1"" of type '" "Tree *""'"); } arg1 = (Tree *)(argp1); free_tree(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_Make_swString) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; swString *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: Make_swString(string);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Make_swString" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (swString *)Make_swString(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_swString, 0 | 0); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_string_edit_distance) { { swString *arg1 = (swString *) 0 ; swString *arg2 = (swString *) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: string_edit_distance(T1,T2);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_swString, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "string_edit_distance" "', argument " "1"" of type '" "swString *""'"); } arg1 = (swString *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_swString, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "string_edit_distance" "', argument " "2"" of type '" "swString *""'"); } arg2 = (swString *)(argp2); result = (float)string_edit_distance(arg1,arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_profile_edit_distance) { { float *arg1 = (float *) 0 ; float *arg2 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: profile_edit_distance(T1,T2);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "profile_edit_distance" "', argument " "1"" of type '" "float const *""'"); } arg1 = (float *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "profile_edit_distance" "', argument " "2"" of type '" "float const *""'"); } arg2 = (float *)(argp2); result = (float)profile_edit_distance((float const *)arg1,(float const *)arg2); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_Make_bp_profile) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; float *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: Make_bp_profile(length);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "Make_bp_profile" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); result = (float *)Make_bp_profile(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_float, SWIG_OWNER | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_Make_bp_profile_bppm) { { double *arg1 = (double *) 0 ; int arg2 ; void *argp1 = 0 ; int res1 = 0 ; int val2 ; int ecode2 = 0 ; int argvi = 0; float *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: Make_bp_profile_bppm(bppm,length);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_double, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Make_bp_profile_bppm" "', argument " "1"" of type '" "double *""'"); } arg1 = (double *)(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 '" "Make_bp_profile_bppm" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); result = (float *)Make_bp_profile_bppm(arg1,arg2); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_float, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_print_bppm) { { float *arg1 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: print_bppm(T);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "print_bppm" "', argument " "1"" of type '" "float const *""'"); } arg1 = (float *)(argp1); print_bppm((float const *)arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_free_profile) { { float *arg1 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: free_profile(T);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "free_profile" "', argument " "1"" of type '" "float *""'"); } arg1 = (float *)(argp1); free_profile(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_space) { { unsigned int arg1 ; unsigned int val1 ; int ecode1 = 0 ; int argvi = 0; void *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: space(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 '" "space" "', argument " "1"" of type '" "unsigned int""'"); } arg1 = (unsigned int)(val1); result = (void *)space(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_void, SWIG_OWNER | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_xrealloc) { { void *arg1 = (void *) 0 ; unsigned int arg2 ; int res1 ; unsigned int val2 ; int ecode2 = 0 ; int argvi = 0; void *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: xrealloc(p,size);"); } res1 = SWIG_ConvertPtr(ST(0),SWIG_as_voidptrptr(&arg1), 0, 0); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "xrealloc" "', argument " "1"" of type '" "void *""'"); } ecode2 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "xrealloc" "', argument " "2"" of type '" "unsigned int""'"); } arg2 = (unsigned int)(val2); result = (void *)xrealloc(arg1,arg2); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_void, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_nrerror) { { char *arg1 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: nrerror(message);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "nrerror" "', argument " "1"" of type '" "char const []""'"); } arg1 = (char *)(buf1); nrerror((char const (*))arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_warn_user) { { char *arg1 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: warn_user(message);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "warn_user" "', argument " "1"" of type '" "char const []""'"); } arg1 = (char *)(buf1); warn_user((char const (*))arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_init_rand) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: init_rand();"); } init_rand(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_urn) { { int argvi = 0; double result; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: urn();"); } result = (double)urn(); ST(argvi) = SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_int_urn) { { int arg1 ; int arg2 ; int val1 ; int ecode1 = 0 ; int val2 ; int ecode2 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: int_urn(from,to);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "int_urn" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "int_urn" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); result = (int)int_urn(arg1,arg2); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_filecopy) { { FILE *arg1 = (FILE *) 0 ; FILE *arg2 = (FILE *) 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: filecopy(from,to);"); } { if (SvOK(ST(0))) /* check for undef */ arg1 = PerlIO_findFILE(IoIFP(sv_2io(ST(0)))); else arg1 = NULL; } { if (SvOK(ST(1))) /* check for undef */ arg2 = PerlIO_findFILE(IoIFP(sv_2io(ST(1)))); else arg2 = NULL; } filecopy(arg1,arg2); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_time_stamp) { { int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: time_stamp();"); } result = (char *)time_stamp(); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; free((char*)result); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_random_string) { { int arg1 ; char *arg2 ; int val1 ; int ecode1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: random_string(l,symbols);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "random_string" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "random_string" "', argument " "2"" of type '" "char const []""'"); } arg2 = (char *)(buf2); result = (char *)random_string(arg1,(char const (*))arg2); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); free((char*)result); XSRETURN(argvi); fail: if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_hamming) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: hamming(s1,s2);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "hamming" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "hamming" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); result = (int)hamming((char const *)arg1,(char const *)arg2); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_hamming_bound) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: hamming_bound(s1,s2,n);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "hamming_bound" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "hamming_bound" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "hamming_bound" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); result = (int)hamming_bound((char const *)arg1,(char const *)arg2,arg3); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_get_line) { { FILE *arg1 = (FILE *) 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: get_line(fp);"); } { if (SvOK(ST(0))) /* check for undef */ arg1 = PerlIO_findFILE(IoIFP(sv_2io(ST(0)))); else arg1 = NULL; } result = (char *)get_line(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; free((char*)result); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_skip_comment_lines) { { char **arg1 = (char **) 0 ; int argvi = 0; int result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: skip_comment_lines(line);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } result = (int)skip_comment_lines(arg1); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; { free(arg1); } XSRETURN(argvi); fail: { free(arg1); } SWIG_croak_null(); } } XS(_wrap_get_input_line) { { char **arg1 = (char **) 0 ; unsigned int arg2 ; unsigned int val2 ; int ecode2 = 0 ; int argvi = 0; unsigned int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: get_input_line(string,options);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } ecode2 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "get_input_line" "', argument " "2"" of type '" "unsigned int""'"); } arg2 = (unsigned int)(val2); result = (unsigned int)get_input_line(arg1,arg2); ST(argvi) = SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(result)); argvi++ ; { free(arg1); } XSRETURN(argvi); fail: { free(arg1); } SWIG_croak_null(); } } XS(_wrap_get_multi_input_line) { { char **arg1 = (char **) 0 ; unsigned int arg2 ; unsigned int val2 ; int ecode2 = 0 ; int argvi = 0; unsigned int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: get_multi_input_line(string,options);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } ecode2 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "get_multi_input_line" "', argument " "2"" of type '" "unsigned int""'"); } arg2 = (unsigned int)(val2); result = (unsigned int)get_multi_input_line(arg1,arg2); ST(argvi) = SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(result)); argvi++ ; { free(arg1); } XSRETURN(argvi); fail: { free(arg1); } SWIG_croak_null(); } } XS(_wrap_read_record) { { char **arg1 = (char **) 0 ; char **arg2 = (char **) 0 ; char ***arg3 = (char ***) 0 ; unsigned int arg4 ; void *argp3 = 0 ; int res3 = 0 ; unsigned int val4 ; int ecode4 = 0 ; int argvi = 0; unsigned int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: read_record(header,sequence,rest,options);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(1))) croak("Argument 2 is not a reference."); if (SvTYPE(SvRV(ST(1))) != SVt_PVAV) croak("Argument 2 is not an array."); tempav = (AV*)SvRV(ST(1)); len = av_len(tempav); arg2 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg2[i] = (char *) SvPV(*tv,PL_na); } arg2[i] = NULL; } res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_p_char, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "read_record" "', argument " "3"" of type '" "char ***""'"); } arg3 = (char ***)(argp3); ecode4 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "read_record" "', argument " "4"" of type '" "unsigned int""'"); } arg4 = (unsigned int)(val4); result = (unsigned int)read_record(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(result)); argvi++ ; { free(arg1); } { free(arg2); } XSRETURN(argvi); fail: { free(arg1); } { free(arg2); } SWIG_croak_null(); } } XS(_wrap_pack_structure) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: pack_structure(struc);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "pack_structure" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); result = (char *)pack_structure((char const *)arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_unpack_structure) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: unpack_structure(packed);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "unpack_structure" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); result = (char *)unpack_structure((char const *)arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); free((char*)result); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_make_pair_table) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; short *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: make_pair_table(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "make_pair_table" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); result = (short *)make_pair_table((char const *)arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_short, SWIG_OWNER | 0); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_copy_pair_table) { { short *arg1 = (short *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; short *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: copy_pair_table(pt);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "copy_pair_table" "', argument " "1"" of type '" "short const *""'"); } arg1 = (short *)(argp1); result = (short *)copy_pair_table((short const *)arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_short, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_bp_distance) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: bp_distance(str1,str2);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "bp_distance" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "bp_distance" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); result = (int)bp_distance((char const *)arg1,(char const *)arg2); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_print_tty_input_seq) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: print_tty_input_seq();"); } print_tty_input_seq(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_print_tty_input_seq_str) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: print_tty_input_seq_str(s);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "print_tty_input_seq_str" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); print_tty_input_seq_str((char const *)arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_print_tty_constraint_full) { { int argvi = 0; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: print_tty_constraint_full();"); } print_tty_constraint_full(); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_print_tty_constraint) { { unsigned int arg1 ; unsigned int val1 ; int ecode1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: print_tty_constraint(option);"); } 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 '" "print_tty_constraint" "', argument " "1"" of type '" "unsigned int""'"); } arg1 = (unsigned int)(val1); print_tty_constraint(arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_str_DNA2RNA) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: str_DNA2RNA(sequence);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "str_DNA2RNA" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); str_DNA2RNA(arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_str_RNA2RNA) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: str_RNA2RNA(sequence);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "str_RNA2RNA" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); str_RNA2RNA(arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_get_iindx) { { unsigned int arg1 ; unsigned int val1 ; int ecode1 = 0 ; int argvi = 0; int *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: get_iindx(length);"); } 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 '" "get_iindx" "', argument " "1"" of type '" "unsigned int""'"); } arg1 = (unsigned int)(val1); result = (int *)get_iindx(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_int, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_indx) { { unsigned int arg1 ; unsigned int val1 ; int ecode1 = 0 ; int argvi = 0; int *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: get_indx(length);"); } 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 '" "get_indx" "', argument " "1"" of type '" "unsigned int""'"); } arg1 = (unsigned int)(val1); result = (int *)get_indx(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_int, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_getConstraint) { { char **arg1 = (char **) 0 ; char **arg2 = (char **) 0 ; unsigned int arg3 ; unsigned int val3 ; int ecode3 = 0 ; int argvi = 0; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: getConstraint(cstruc,lines,option);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(1))) croak("Argument 2 is not a reference."); if (SvTYPE(SvRV(ST(1))) != SVt_PVAV) croak("Argument 2 is not an array."); tempav = (AV*)SvRV(ST(1)); len = av_len(tempav); arg2 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg2[i] = (char *) SvPV(*tv,PL_na); } arg2[i] = NULL; } ecode3 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "getConstraint" "', argument " "3"" of type '" "unsigned int""'"); } arg3 = (unsigned int)(val3); getConstraint(arg1,(char const **)arg2,arg3); ST(argvi) = sv_newmortal(); { free(arg1); } { free(arg2); } XSRETURN(argvi); fail: { free(arg1); } { free(arg2); } SWIG_croak_null(); } } XS(_wrap_constrain_ptypes) { { char *arg1 = (char *) 0 ; unsigned int arg2 ; char *arg3 = (char *) 0 ; int *arg4 = (int *) 0 ; int arg5 ; unsigned int arg6 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; unsigned int val2 ; int ecode2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int val5 ; int ecode5 = 0 ; unsigned int val6 ; int ecode6 = 0 ; int argvi = 0; dXSARGS; if ((items < 6) || (items > 6)) { SWIG_croak("Usage: constrain_ptypes(constraint,length,ptype,BP,min_loop_size,idx_type);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "constrain_ptypes" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); ecode2 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "constrain_ptypes" "', argument " "2"" of type '" "unsigned int""'"); } arg2 = (unsigned int)(val2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "constrain_ptypes" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_int, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "constrain_ptypes" "', argument " "4"" of type '" "int *""'"); } arg4 = (int *)(argp4); ecode5 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(4), &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "constrain_ptypes" "', argument " "5"" of type '" "int""'"); } arg5 = (int)(val5); ecode6 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(5), &val6); if (!SWIG_IsOK(ecode6)) { SWIG_exception_fail(SWIG_ArgError(ecode6), "in method '" "constrain_ptypes" "', argument " "6"" of type '" "unsigned int""'"); } arg6 = (unsigned int)(val6); constrain_ptypes((char const *)arg1,arg2,arg3,arg4,arg5,arg6); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_make_referenceBP_array) { { short *arg1 = (short *) 0 ; unsigned int arg2 ; void *argp1 = 0 ; int res1 = 0 ; unsigned int val2 ; int ecode2 = 0 ; int argvi = 0; unsigned int *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: make_referenceBP_array(reference_pt,turn);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "make_referenceBP_array" "', argument " "1"" of type '" "short *""'"); } arg1 = (short *)(argp1); ecode2 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "make_referenceBP_array" "', argument " "2"" of type '" "unsigned int""'"); } arg2 = (unsigned int)(val2); result = (unsigned int *)make_referenceBP_array(arg1,arg2); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_unsigned_int, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_compute_BPdifferences) { { short *arg1 = (short *) 0 ; short *arg2 = (short *) 0 ; unsigned int arg3 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; unsigned int val3 ; int ecode3 = 0 ; int argvi = 0; unsigned int *result = 0 ; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: compute_BPdifferences(pt1,pt2,turn);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "compute_BPdifferences" "', argument " "1"" of type '" "short *""'"); } arg1 = (short *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "compute_BPdifferences" "', argument " "2"" of type '" "short *""'"); } arg2 = (short *)(argp2); ecode3 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "compute_BPdifferences" "', argument " "3"" of type '" "unsigned int""'"); } arg3 = (unsigned int)(val3); result = (unsigned int *)compute_BPdifferences(arg1,arg2,arg3); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_unsigned_int, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_read_parameter_file) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: read_parameter_file(fname);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "read_parameter_file" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); read_parameter_file(arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_write_parameter_file) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: write_parameter_file(fname);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "write_parameter_file" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); write_parameter_file(arg1); ST(argvi) = sv_newmortal(); if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_deref_any) { { void **arg1 = (void **) 0 ; int arg2 ; void *argp1 = 0 ; int res1 = 0 ; int val2 ; int ecode2 = 0 ; int argvi = 0; void *result = 0 ; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: deref_any(ptr,index);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_p_void, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "deref_any" "', argument " "1"" of type '" "void **""'"); } arg1 = (void **)(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 '" "deref_any" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); result = (void *)deref_any(arg1,arg2); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_void, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_scale_parameters) { { int argvi = 0; paramT *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: scale_parameters();"); } result = (paramT *)scale_parameters(); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_paramT, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_copy_parameters) { { int argvi = 0; paramT *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: copy_parameters();"); } result = (paramT *)copy_parameters(); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_paramT, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_set_parameters) { { paramT *arg1 = (paramT *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; paramT *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: set_parameters(dest);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_paramT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "set_parameters" "', argument " "1"" of type '" "paramT *""'"); } arg1 = (paramT *)(argp1); result = (paramT *)set_parameters(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_paramT, 0 | 0); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_get_aligned_line) { { int arg1 ; int val1 ; int ecode1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: get_aligned_line(int);"); } ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1); if (!SWIG_IsOK(ecode1)) { SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "get_aligned_line" "', argument " "1"" of type '" "int""'"); } arg1 = (int)(val1); result = (char *)get_aligned_line(arg1); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_make_loop_index) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; short *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: make_loop_index(structure);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "make_loop_index" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); result = (short *)make_loop_index((char const *)arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_short, 0 | 0); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_energy_of_move) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int arg3 ; int arg4 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int val4 ; int ecode4 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: energy_of_move(string,structure,mi,mj);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "energy_of_move" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "energy_of_move" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "energy_of_move" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "energy_of_move" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); result = (float)energy_of_move((char const *)arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_duplexT_i_set) { { duplexT *arg1 = (duplexT *) 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: duplexT_i_set(self,i);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_i_set" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(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 '" "duplexT_i_set" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); if (arg1) (arg1)->i = arg2; ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_duplexT_i_get) { { duplexT *arg1 = (duplexT *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: duplexT_i_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_i_get" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(argp1); result = (int) ((arg1)->i); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_duplexT_j_set) { { duplexT *arg1 = (duplexT *) 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: duplexT_j_set(self,j);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_j_set" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(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 '" "duplexT_j_set" "', argument " "2"" of type '" "int""'"); } arg2 = (int)(val2); if (arg1) (arg1)->j = arg2; ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_duplexT_j_get) { { duplexT *arg1 = (duplexT *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: duplexT_j_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_j_get" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(argp1); result = (int) ((arg1)->j); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_duplexT_structure_set) { { duplexT *arg1 = (duplexT *) 0 ; char *arg2 = (char *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: duplexT_structure_set(self,structure);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_structure_set" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(argp1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "duplexT_structure_set" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); if (arg1->structure) free((char*)arg1->structure); if (arg2) { size_t size = strlen((const char *)(arg2)) + 1; arg1->structure = (char *)(char *)memcpy((char *)malloc((size)*sizeof(char)), (const char *)(arg2), sizeof(char)*(size)); } else { arg1->structure = 0; } ST(argvi) = sv_newmortal(); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_duplexT_structure_get) { { duplexT *arg1 = (duplexT *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; char *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: duplexT_structure_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_structure_get" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(argp1); result = (char *) ((arg1)->structure); ST(argvi) = SWIG_FromCharPtr((const char *)result); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_duplexT_energy_set) { { duplexT *arg1 = (duplexT *) 0 ; float arg2 ; void *argp1 = 0 ; int res1 = 0 ; float val2 ; int ecode2 = 0 ; int argvi = 0; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: duplexT_energy_set(self,energy);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_energy_set" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(argp1); ecode2 = SWIG_AsVal_float SWIG_PERL_CALL_ARGS_2(ST(1), &val2); if (!SWIG_IsOK(ecode2)) { SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "duplexT_energy_set" "', argument " "2"" of type '" "float""'"); } arg2 = (float)(val2); if (arg1) (arg1)->energy = arg2; ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_duplexT_energy_get) { { duplexT *arg1 = (duplexT *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: duplexT_energy_get(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexT_energy_get" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(argp1); result = (float) ((arg1)->energy); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_new_duplexT) { { int argvi = 0; duplexT *result = 0 ; dXSARGS; if ((items < 0) || (items > 0)) { SWIG_croak("Usage: new_duplexT();"); } result = (duplexT *)calloc(1, sizeof(duplexT)); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_duplexT, SWIG_OWNER | SWIG_SHADOW); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_delete_duplexT) { { duplexT *arg1 = (duplexT *) 0 ; void *argp1 = 0 ; int res1 = 0 ; int argvi = 0; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: delete_duplexT(self);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_duplexT, SWIG_POINTER_DISOWN | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_duplexT" "', argument " "1"" of type '" "duplexT *""'"); } arg1 = (duplexT *)(argp1); free((char *) arg1); ST(argvi) = sv_newmortal(); XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_duplexfold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; duplexT result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: duplexfold(s1,s2);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "duplexfold" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "duplexfold" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); result = duplexfold((char const *)arg1,(char const *)arg2); ST(argvi) = SWIG_NewPointerObj((duplexT *)memcpy((duplexT *)malloc(sizeof(duplexT)),&result,sizeof(duplexT)), SWIGTYPE_p_duplexT, SWIG_POINTER_OWN | SWIG_SHADOW); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_aliduplexfold) { { char **arg1 = (char **) 0 ; char **arg2 = (char **) 0 ; int argvi = 0; duplexT result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: aliduplexfold(s1,s2);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(1))) croak("Argument 2 is not a reference."); if (SvTYPE(SvRV(ST(1))) != SVt_PVAV) croak("Argument 2 is not an array."); tempav = (AV*)SvRV(ST(1)); len = av_len(tempav); arg2 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg2[i] = (char *) SvPV(*tv,PL_na); } arg2[i] = NULL; } result = aliduplexfold((char const **)arg1,(char const **)arg2); ST(argvi) = SWIG_NewPointerObj((duplexT *)memcpy((duplexT *)malloc(sizeof(duplexT)),&result,sizeof(duplexT)), SWIGTYPE_p_duplexT, SWIG_POINTER_OWN | SWIG_SHADOW); argvi++ ; { free(arg1); } { free(arg2); } XSRETURN(argvi); fail: { free(arg1); } { free(arg2); } SWIG_croak_null(); } } XS(_wrap_encode_seq) { { char *arg1 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int argvi = 0; short *result = 0 ; dXSARGS; if ((items < 1) || (items > 1)) { SWIG_croak("Usage: encode_seq(sequence);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "encode_seq" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); result = (short *)encode_seq(arg1); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_short, 0 | 0); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); SWIG_croak_null(); } } XS(_wrap_Lfold) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int arg3 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: Lfold(string,structure,maxdist);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Lfold" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "Lfold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "Lfold" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); result = (float)Lfold((char const *)arg1,arg2,arg3); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_aliLfold) { { char **arg1 = (char **) 0 ; char *arg2 = (char *) 0 ; int arg3 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: aliLfold(strings,structure,maxdist);"); } { AV *tempav; I32 len; int i; SV **tv; if (!SvROK(ST(0))) croak("Argument 1 is not a reference."); if (SvTYPE(SvRV(ST(0))) != SVt_PVAV) croak("Argument 1 is not an array."); tempav = (AV*)SvRV(ST(0)); len = av_len(tempav); arg1 = (char **) malloc((len+2)*sizeof(char *)); for (i = 0; i <= len; i++) { tv = av_fetch(tempav, i, 0); arg1[i] = (char *) SvPV(*tv,PL_na); } arg1[i] = NULL; } res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "aliLfold" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "aliLfold" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); result = (float)aliLfold((char const **)arg1,arg2,arg3); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: { free(arg1); } if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_Lfoldz) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int arg3 ; int arg4 ; double arg5 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int val3 ; int ecode3 = 0 ; int val4 ; int ecode4 = 0 ; double val5 ; int ecode5 = 0 ; int argvi = 0; float result; dXSARGS; if ((items < 5) || (items > 5)) { SWIG_croak("Usage: Lfoldz(string,structure,maxdist,zsc,min_z);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Lfoldz" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "Lfoldz" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); ecode3 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(2), &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "Lfoldz" "', argument " "3"" of type '" "int""'"); } arg3 = (int)(val3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "Lfoldz" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); ecode5 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(4), &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "Lfoldz" "', argument " "5"" of type '" "double""'"); } arg5 = (double)(val5); result = (float)Lfoldz((char const *)arg1,arg2,arg3,arg4,arg5); ST(argvi) = SWIG_From_float SWIG_PERL_CALL_ARGS_1((float)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_PS_rna_plot) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: PS_rna_plot(string,structure,file);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_rna_plot" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_rna_plot" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "PS_rna_plot" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); result = (int)PS_rna_plot(arg1,arg2,arg3); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_PS_rna_plot_a) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; char *arg4 = (char *) 0 ; char *arg5 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int res4 ; char *buf4 = 0 ; int alloc4 = 0 ; int res5 ; char *buf5 = 0 ; int alloc5 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 5) || (items > 5)) { SWIG_croak("Usage: PS_rna_plot_a(string,structure,file,pre,post);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_rna_plot_a" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_rna_plot_a" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "PS_rna_plot_a" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); res4 = SWIG_AsCharPtrAndSize(ST(3), &buf4, NULL, &alloc4); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "PS_rna_plot_a" "', argument " "4"" of type '" "char *""'"); } arg4 = (char *)(buf4); res5 = SWIG_AsCharPtrAndSize(ST(4), &buf5, NULL, &alloc5); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "PS_rna_plot_a" "', argument " "5"" of type '" "char *""'"); } arg5 = (char *)(buf5); result = (int)PS_rna_plot_a(arg1,arg2,arg3,arg4,arg5); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); if (alloc4 == SWIG_NEWOBJ) free((char*)buf4); if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); if (alloc4 == SWIG_NEWOBJ) free((char*)buf4); if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); SWIG_croak_null(); } } XS(_wrap_gmlRNA) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; char arg4 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; char val4 ; int ecode4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: gmlRNA(string,structure,ssfile,option);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "gmlRNA" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "gmlRNA" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "gmlRNA" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); ecode4 = SWIG_AsVal_char SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "gmlRNA" "', argument " "4"" of type '" "char""'"); } arg4 = (char)(val4); result = (int)gmlRNA(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_ssv_rna_plot) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: ssv_rna_plot(string,structure,ssfile);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "ssv_rna_plot" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "ssv_rna_plot" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "ssv_rna_plot" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); result = (int)ssv_rna_plot(arg1,arg2,arg3); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_svg_rna_plot) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: svg_rna_plot(string,structure,ssfile);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "svg_rna_plot" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "svg_rna_plot" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "svg_rna_plot" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); result = (int)svg_rna_plot(arg1,arg2,arg3); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_xrna_plot) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: xrna_plot(string,structure,ssfile);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "xrna_plot" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "xrna_plot" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "xrna_plot" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); result = (int)xrna_plot(arg1,arg2,arg3); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_PS_color_dot_plot) { { char *arg1 = (char *) 0 ; cpair *arg2 = (cpair *) 0 ; char *arg3 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: PS_color_dot_plot(string,pi,filename);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_color_dot_plot" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_cpair, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_color_dot_plot" "', argument " "2"" of type '" "cpair *""'"); } arg2 = (cpair *)(argp2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "PS_color_dot_plot" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); result = (int)PS_color_dot_plot(arg1,arg2,arg3); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_PS_color_dot_plot_turn) { { char *arg1 = (char *) 0 ; cpair *arg2 = (cpair *) 0 ; char *arg3 = (char *) 0 ; int arg4 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int val4 ; int ecode4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: PS_color_dot_plot_turn(seq,pi,filename,winSize);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_color_dot_plot_turn" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_cpair, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_color_dot_plot_turn" "', argument " "2"" of type '" "cpair *""'"); } arg2 = (cpair *)(argp2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "PS_color_dot_plot_turn" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "PS_color_dot_plot_turn" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); result = (int)PS_color_dot_plot_turn(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_PS_dot_plot_list) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; plist *arg3 = (plist *) 0 ; plist *arg4 = (plist *) 0 ; char *arg5 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int res5 ; char *buf5 = 0 ; int alloc5 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 5) || (items > 5)) { SWIG_croak("Usage: PS_dot_plot_list(seq,filename,pl,mf,comment);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_dot_plot_list" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_dot_plot_list" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_plist, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "PS_dot_plot_list" "', argument " "3"" of type '" "plist *""'"); } arg3 = (plist *)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_plist, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "PS_dot_plot_list" "', argument " "4"" of type '" "plist *""'"); } arg4 = (plist *)(argp4); res5 = SWIG_AsCharPtrAndSize(ST(4), &buf5, NULL, &alloc5); if (!SWIG_IsOK(res5)) { SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "PS_dot_plot_list" "', argument " "5"" of type '" "char *""'"); } arg5 = (char *)(buf5); result = (int)PS_dot_plot_list(arg1,arg2,arg3,arg4,arg5); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc5 == SWIG_NEWOBJ) free((char*)buf5); SWIG_croak_null(); } } XS(_wrap_PS_dot_plot_turn) { { char *arg1 = (char *) 0 ; struct plist *arg2 = (struct plist *) 0 ; char *arg3 = (char *) 0 ; int arg4 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int val4 ; int ecode4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: PS_dot_plot_turn(seq,pl,filename,winSize);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_dot_plot_turn" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_plist, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_dot_plot_turn" "', argument " "2"" of type '" "struct plist *""'"); } arg2 = (struct plist *)(argp2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "PS_dot_plot_turn" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "PS_dot_plot_turn" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); result = (int)PS_dot_plot_turn(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_PS_color_aln) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char **arg3 ; char **arg4 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; void *argp4 = 0 ; int res4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: PS_color_aln(structure,filename,seqs,names);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_color_aln" "', argument " "1"" of type '" "char const *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_color_aln" "', argument " "2"" of type '" "char const *""'"); } arg2 = (char *)(buf2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_p_char, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "PS_color_aln" "', argument " "3"" of type '" "char const *[]""'"); } arg3 = (char **)(argp3); res4 = SWIG_ConvertPtr(ST(3), &argp4,SWIGTYPE_p_p_char, 0 | 0 ); if (!SWIG_IsOK(res4)) { SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "PS_color_aln" "', argument " "4"" of type '" "char const *[]""'"); } arg4 = (char **)(argp4); result = (int)PS_color_aln((char const *)arg1,(char const *)arg2,(char const *(*))arg3,(char const *(*))arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_simple_xy_coordinates) { { short *arg1 = (short *) 0 ; float *arg2 = (float *) 0 ; float *arg3 = (float *) 0 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 = 0 ; int res2 = 0 ; void *argp3 = 0 ; int res3 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 3) || (items > 3)) { SWIG_croak("Usage: simple_xy_coordinates(pair_table,X,Y);"); } res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_short, 0 | 0 ); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "simple_xy_coordinates" "', argument " "1"" of type '" "short *""'"); } arg1 = (short *)(argp1); res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "simple_xy_coordinates" "', argument " "2"" of type '" "float *""'"); } arg2 = (float *)(argp2); res3 = SWIG_ConvertPtr(ST(2), &argp3,SWIGTYPE_p_float, 0 | 0 ); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "simple_xy_coordinates" "', argument " "3"" of type '" "float *""'"); } arg3 = (float *)(argp3); result = (int)simple_xy_coordinates(arg1,arg2,arg3); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; XSRETURN(argvi); fail: SWIG_croak_null(); } } XS(_wrap_PS_dot_plot) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 2) || (items > 2)) { SWIG_croak("Usage: PS_dot_plot(string,file);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PS_dot_plot" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "PS_dot_plot" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); result = (int)PS_dot_plot(arg1,arg2); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); SWIG_croak_null(); } } XS(_wrap_find_saddle) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; int arg4 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int val4 ; int ecode4 = 0 ; int argvi = 0; int result; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: find_saddle(seq,struc1,struc2,max);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "find_saddle" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "find_saddle" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "find_saddle" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "find_saddle" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); result = (int)find_saddle(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1((int)(result)); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } XS(_wrap_get_path) { { char *arg1 = (char *) 0 ; char *arg2 = (char *) 0 ; char *arg3 = (char *) 0 ; int arg4 ; int res1 ; char *buf1 = 0 ; int alloc1 = 0 ; int res2 ; char *buf2 = 0 ; int alloc2 = 0 ; int res3 ; char *buf3 = 0 ; int alloc3 = 0 ; int val4 ; int ecode4 = 0 ; int argvi = 0; path_t *result = 0 ; dXSARGS; if ((items < 4) || (items > 4)) { SWIG_croak("Usage: get_path(seq,s1,s2,maxkeep);"); } res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, NULL, &alloc1); if (!SWIG_IsOK(res1)) { SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "get_path" "', argument " "1"" of type '" "char *""'"); } arg1 = (char *)(buf1); res2 = SWIG_AsCharPtrAndSize(ST(1), &buf2, NULL, &alloc2); if (!SWIG_IsOK(res2)) { SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "get_path" "', argument " "2"" of type '" "char *""'"); } arg2 = (char *)(buf2); res3 = SWIG_AsCharPtrAndSize(ST(2), &buf3, NULL, &alloc3); if (!SWIG_IsOK(res3)) { SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "get_path" "', argument " "3"" of type '" "char *""'"); } arg3 = (char *)(buf3); ecode4 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(3), &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "get_path" "', argument " "4"" of type '" "int""'"); } arg4 = (int)(val4); result = (path_t *)get_path(arg1,arg2,arg3,arg4); ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_path_t, 0 | 0); argvi++ ; if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); XSRETURN(argvi); fail: if (alloc1 == SWIG_NEWOBJ) free((char*)buf1); if (alloc2 == SWIG_NEWOBJ) free((char*)buf2); if (alloc3 == SWIG_NEWOBJ) free((char*)buf3); SWIG_croak_null(); } } /* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */ static void *_p_p_floatArrayTo_p_p_float(void *x, int *SWIGUNUSEDPARM(newmemory)) { return (void *)((float **) ((floatArray **) x)); } static void *_p_floatArrayTo_p_float(void *x, int *SWIGUNUSEDPARM(newmemory)) { return (void *)((float *) ((floatArray *) x)); } static void *_p_intArrayTo_p_int(void *x, int *SWIGUNUSEDPARM(newmemory)) { return (void *)((int *) ((intArray *) x)); } static void *_p_doubleArrayTo_p_double(void *x, int *SWIGUNUSEDPARM(newmemory)) { return (void *)((double *) ((doubleArray *) x)); } static void *_p_p_doubleArrayTo_p_p_double(void *x, int *SWIGUNUSEDPARM(newmemory)) { return (void *)((double **) ((doubleArray **) x)); } static void *_p_p_intArrayTo_p_p_int(void *x, int *SWIGUNUSEDPARM(newmemory)) { return (void *)((int **) ((intArray **) x)); } static swig_type_info _swigt__p_COORDINATE = {"_p_COORDINATE", "COORDINATE *", 0, 0, (void*)"RNA::COORDINATE", 0}; static swig_type_info _swigt__p_ConcEnt = {"_p_ConcEnt", "ConcEnt *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_FILE = {"_p_FILE", "FILE *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_SOLUTION = {"_p_SOLUTION", "SOLUTION *", 0, 0, (void*)"RNA::SOLUTION", 0}; static swig_type_info _swigt__p_Tree = {"_p_Tree", "Tree *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_bondT = {"_p_bondT", "bondT *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_char = {"_p_char", "char *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_cpair = {"_p_cpair", "cpair *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_double = {"_p_double", "double *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_doubleArray = {"_p_doubleArray", "struct doubleArray *|doubleArray *", 0, 0, (void*)"RNA::doubleArray", 0}; static swig_type_info _swigt__p_duplexT = {"_p_duplexT", "duplexT *", 0, 0, (void*)"RNA::duplexT", 0}; static swig_type_info _swigt__p_float = {"_p_float", "float *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_floatArray = {"_p_floatArray", "struct floatArray *|floatArray *", 0, 0, (void*)"RNA::floatArray", 0}; static swig_type_info _swigt__p_int = {"_p_int", "int *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_intArray = {"_p_intArray", "struct intArray *|intArray *", 0, 0, (void*)"RNA::intArray", 0}; static swig_type_info _swigt__p_p_char = {"_p_p_char", "char **", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_double = {"_p_p_double", "double **", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_doubleArray = {"_p_p_doubleArray", 0, 0, 0, 0, 0}; static swig_type_info _swigt__p_p_float = {"_p_p_float", "float **", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_floatArray = {"_p_p_floatArray", 0, 0, 0, 0, 0}; static swig_type_info _swigt__p_p_int = {"_p_p_int", "int **", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_intArray = {"_p_p_intArray", 0, 0, 0, 0, 0}; static swig_type_info _swigt__p_p_p_char = {"_p_p_p_char", "char ***", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_p_short = {"_p_p_p_short", "short ***", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_p_unsigned_short = {"_p_p_p_unsigned_short", "unsigned short ***", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_plist = {"_p_p_plist", "plist **", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_short = {"_p_p_short", "short **", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_p_void = {"_p_p_void", "void **", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_paramT = {"_p_paramT", "paramT *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_path_t = {"_p_path_t", "path_t *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_plist = {"_p_plist", "plist *|struct plist *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_short = {"_p_short", "short *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_swString = {"_p_swString", "swString *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_unsigned_int = {"_p_unsigned_int", "unsigned int *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_unsigned_short = {"_p_unsigned_short", "unsigned short *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_void = {"_p_void", "void *", 0, 0, (void*)0, 0}; static swig_type_info *swig_type_initial[] = { &_swigt__p_COORDINATE, &_swigt__p_ConcEnt, &_swigt__p_FILE, &_swigt__p_SOLUTION, &_swigt__p_Tree, &_swigt__p_bondT, &_swigt__p_char, &_swigt__p_cpair, &_swigt__p_double, &_swigt__p_doubleArray, &_swigt__p_duplexT, &_swigt__p_float, &_swigt__p_floatArray, &_swigt__p_int, &_swigt__p_intArray, &_swigt__p_p_char, &_swigt__p_p_double, &_swigt__p_p_doubleArray, &_swigt__p_p_float, &_swigt__p_p_floatArray, &_swigt__p_p_int, &_swigt__p_p_intArray, &_swigt__p_p_p_char, &_swigt__p_p_p_short, &_swigt__p_p_p_unsigned_short, &_swigt__p_p_plist, &_swigt__p_p_short, &_swigt__p_p_void, &_swigt__p_paramT, &_swigt__p_path_t, &_swigt__p_plist, &_swigt__p_short, &_swigt__p_swString, &_swigt__p_unsigned_int, &_swigt__p_unsigned_short, &_swigt__p_void, }; static swig_cast_info _swigc__p_COORDINATE[] = { {&_swigt__p_COORDINATE, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_ConcEnt[] = { {&_swigt__p_ConcEnt, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_FILE[] = { {&_swigt__p_FILE, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_SOLUTION[] = { {&_swigt__p_SOLUTION, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_Tree[] = { {&_swigt__p_Tree, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_bondT[] = { {&_swigt__p_bondT, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_char[] = { {&_swigt__p_char, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_cpair[] = { {&_swigt__p_cpair, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_double[] = { {&_swigt__p_doubleArray, _p_doubleArrayTo_p_double, 0, 0}, {&_swigt__p_double, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_doubleArray[] = { {&_swigt__p_doubleArray, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_duplexT[] = { {&_swigt__p_duplexT, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_float[] = { {&_swigt__p_float, 0, 0, 0}, {&_swigt__p_floatArray, _p_floatArrayTo_p_float, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_floatArray[] = { {&_swigt__p_floatArray, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_int[] = { {&_swigt__p_intArray, _p_intArrayTo_p_int, 0, 0}, {&_swigt__p_int, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_intArray[] = { {&_swigt__p_intArray, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_char[] = { {&_swigt__p_p_char, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_doubleArray[] = {{&_swigt__p_p_doubleArray, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_double[] = { {&_swigt__p_p_doubleArray, _p_p_doubleArrayTo_p_p_double, 0, 0}, {&_swigt__p_p_double, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_floatArray[] = {{&_swigt__p_p_floatArray, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_float[] = { {&_swigt__p_p_float, 0, 0, 0}, {&_swigt__p_p_floatArray, _p_p_floatArrayTo_p_p_float, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_intArray[] = {{&_swigt__p_p_intArray, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_int[] = { {&_swigt__p_p_intArray, _p_p_intArrayTo_p_p_int, 0, 0}, {&_swigt__p_p_int, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_p_char[] = { {&_swigt__p_p_p_char, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_p_short[] = { {&_swigt__p_p_p_short, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_p_unsigned_short[] = { {&_swigt__p_p_p_unsigned_short, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_plist[] = { {&_swigt__p_p_plist, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_short[] = { {&_swigt__p_p_short, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_p_void[] = { {&_swigt__p_p_void, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_paramT[] = { {&_swigt__p_paramT, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_path_t[] = { {&_swigt__p_path_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_plist[] = { {&_swigt__p_plist, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_short[] = { {&_swigt__p_short, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_swString[] = { {&_swigt__p_swString, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_unsigned_int[] = { {&_swigt__p_unsigned_int, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_unsigned_short[] = { {&_swigt__p_unsigned_short, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_void[] = { {&_swigt__p_void, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info *swig_cast_initial[] = { _swigc__p_COORDINATE, _swigc__p_ConcEnt, _swigc__p_FILE, _swigc__p_SOLUTION, _swigc__p_Tree, _swigc__p_bondT, _swigc__p_char, _swigc__p_cpair, _swigc__p_double, _swigc__p_doubleArray, _swigc__p_duplexT, _swigc__p_float, _swigc__p_floatArray, _swigc__p_int, _swigc__p_intArray, _swigc__p_p_char, _swigc__p_p_double, _swigc__p_p_doubleArray, _swigc__p_p_float, _swigc__p_p_floatArray, _swigc__p_p_int, _swigc__p_p_intArray, _swigc__p_p_p_char, _swigc__p_p_p_short, _swigc__p_p_p_unsigned_short, _swigc__p_p_plist, _swigc__p_p_short, _swigc__p_p_void, _swigc__p_paramT, _swigc__p_path_t, _swigc__p_plist, _swigc__p_short, _swigc__p_swString, _swigc__p_unsigned_int, _swigc__p_unsigned_short, _swigc__p_void, }; /* -------- 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[] = { { "RNAc::logML", MAGIC_CLASS _wrap_logML_set, MAGIC_CLASS _wrap_logML_get,0 }, { "RNAc::uniq_ML", MAGIC_CLASS _wrap_uniq_ML_set, MAGIC_CLASS _wrap_uniq_ML_get,0 }, { "RNAc::cut_point", MAGIC_CLASS _wrap_cut_point_set, MAGIC_CLASS _wrap_cut_point_get,0 }, { "RNAc::eos_debug", MAGIC_CLASS _wrap_eos_debug_set, MAGIC_CLASS _wrap_eos_debug_get,0 }, { "RNAc::st_back", MAGIC_CLASS _wrap_st_back_set, MAGIC_CLASS _wrap_st_back_get,0 }, { "RNAc::mirnatog", MAGIC_CLASS _wrap_mirnatog_set, MAGIC_CLASS _wrap_mirnatog_get,0 }, { "RNAc::F_monomer", MAGIC_CLASS _wrap_F_monomer_set, MAGIC_CLASS _wrap_F_monomer_get,&SWIGTYPE_p_double }, { "RNAc::symbolset", MAGIC_CLASS _wrap_symbolset_set, MAGIC_CLASS _wrap_symbolset_get,0 }, { "RNAc::final_cost", MAGIC_CLASS _wrap_final_cost_set, MAGIC_CLASS _wrap_final_cost_get,0 }, { "RNAc::give_up", MAGIC_CLASS _wrap_give_up_set, MAGIC_CLASS _wrap_give_up_get,0 }, { "RNAc::inv_verbose", MAGIC_CLASS _wrap_inv_verbose_set, MAGIC_CLASS _wrap_inv_verbose_get,0 }, { "RNAc::fold_constrained", MAGIC_CLASS _wrap_fold_constrained_set, MAGIC_CLASS _wrap_fold_constrained_get,0 }, { "RNAc::noLonelyPairs", MAGIC_CLASS _wrap_noLonelyPairs_set, MAGIC_CLASS _wrap_noLonelyPairs_get,0 }, { "RNAc::dangles", MAGIC_CLASS _wrap_dangles_set, MAGIC_CLASS _wrap_dangles_get,0 }, { "RNAc::noGU", MAGIC_CLASS _wrap_noGU_set, MAGIC_CLASS _wrap_noGU_get,0 }, { "RNAc::no_closingGU", MAGIC_CLASS _wrap_no_closingGU_set, MAGIC_CLASS _wrap_no_closingGU_get,0 }, { "RNAc::tetra_loop", MAGIC_CLASS _wrap_tetra_loop_set, MAGIC_CLASS _wrap_tetra_loop_get,0 }, { "RNAc::energy_set", MAGIC_CLASS _wrap_energy_set_set, MAGIC_CLASS _wrap_energy_set_get,0 }, { "RNAc::circ", MAGIC_CLASS _wrap_circ_set, MAGIC_CLASS _wrap_circ_get,0 }, { "RNAc::csv", MAGIC_CLASS _wrap_csv_set, MAGIC_CLASS _wrap_csv_get,0 }, { "RNAc::oldAliEn", MAGIC_CLASS _wrap_oldAliEn_set, MAGIC_CLASS _wrap_oldAliEn_get,0 }, { "RNAc::ribo", MAGIC_CLASS _wrap_ribo_set, MAGIC_CLASS _wrap_ribo_get,0 }, { "RNAc::RibosumFile", MAGIC_CLASS _wrap_RibosumFile_set, MAGIC_CLASS _wrap_RibosumFile_get,0 }, { "RNAc::nonstandards", MAGIC_CLASS _wrap_nonstandards_set, MAGIC_CLASS _wrap_nonstandards_get,0 }, { "RNAc::temperature", MAGIC_CLASS _wrap_temperature_set, MAGIC_CLASS _wrap_temperature_get,0 }, { "RNAc::james_rule", MAGIC_CLASS _wrap_james_rule_set, MAGIC_CLASS _wrap_james_rule_get,0 }, { "RNAc::base_pair", MAGIC_CLASS _wrap_base_pair_set, MAGIC_CLASS _wrap_base_pair_get,&SWIGTYPE_p_bondT }, { "RNAc::pr", MAGIC_CLASS _wrap_pr_set, MAGIC_CLASS _wrap_pr_get,&SWIGTYPE_p_double }, { "RNAc::iindx", MAGIC_CLASS _wrap_iindx_set, MAGIC_CLASS _wrap_iindx_get,&SWIGTYPE_p_int }, { "RNAc::pf_scale", MAGIC_CLASS _wrap_pf_scale_set, MAGIC_CLASS _wrap_pf_scale_get,0 }, { "RNAc::do_backtrack", MAGIC_CLASS _wrap_do_backtrack_set, MAGIC_CLASS _wrap_do_backtrack_get,0 }, { "RNAc::backtrack_type", MAGIC_CLASS _wrap_backtrack_type_set, MAGIC_CLASS _wrap_backtrack_type_get,0 }, { "RNAc::cv_fact", MAGIC_CLASS _wrap_cv_fact_set, MAGIC_CLASS _wrap_cv_fact_get,0 }, { "RNAc::nc_fact", MAGIC_CLASS _wrap_nc_fact_set, MAGIC_CLASS _wrap_nc_fact_get,0 }, { "RNAc::subopt_sorted", MAGIC_CLASS _wrap_subopt_sorted_set, MAGIC_CLASS _wrap_subopt_sorted_get,0 }, { "RNAc::loop_size", MAGIC_CLASS _wrap_loop_size_set, MAGIC_CLASS _wrap_loop_size_get,&SWIGTYPE_p_int }, { "RNAc::helix_size", MAGIC_CLASS _wrap_helix_size_set, MAGIC_CLASS _wrap_helix_size_get,&SWIGTYPE_p_int }, { "RNAc::loop_degree", MAGIC_CLASS _wrap_loop_degree_set, MAGIC_CLASS _wrap_loop_degree_get,&SWIGTYPE_p_int }, { "RNAc::loops", MAGIC_CLASS _wrap_loops_set, MAGIC_CLASS _wrap_loops_get,0 }, { "RNAc::unpaired", MAGIC_CLASS _wrap_unpaired_set, MAGIC_CLASS _wrap_unpaired_get,0 }, { "RNAc::pairs", MAGIC_CLASS _wrap_pairs_set, MAGIC_CLASS _wrap_pairs_get,0 }, { "RNAc::edit_backtrack", MAGIC_CLASS _wrap_edit_backtrack_set, MAGIC_CLASS _wrap_edit_backtrack_get,0 }, { "RNAc::aligned_line", MAGIC_CLASS _wrap_aligned_line_set, MAGIC_CLASS _wrap_aligned_line_get,&SWIGTYPE_p_p_char }, { "RNAc::cost_matrix", MAGIC_CLASS _wrap_cost_matrix_set, MAGIC_CLASS _wrap_cost_matrix_get,0 }, { "RNAc::xsubi", MAGIC_CLASS _wrap_xsubi_set, MAGIC_CLASS _wrap_xsubi_get,&SWIGTYPE_p_unsigned_short }, { "RNAc::rna_plot_type", MAGIC_CLASS _wrap_rna_plot_type_set, MAGIC_CLASS _wrap_rna_plot_type_get,0 }, {0,0,0,0} }; static swig_command_info swig_commands[] = { {"RNAc::new_intP", _wrap_new_intP}, {"RNAc::delete_intP", _wrap_delete_intP}, {"RNAc::intP_getitem", _wrap_intP_getitem}, {"RNAc::intP_setitem", _wrap_intP_setitem}, {"RNAc::new_intArray", _wrap_new_intArray}, {"RNAc::delete_intArray", _wrap_delete_intArray}, {"RNAc::intArray_getitem", _wrap_intArray_getitem}, {"RNAc::intArray_setitem", _wrap_intArray_setitem}, {"RNAc::intArray_cast", _wrap_intArray_cast}, {"RNAc::intArray_frompointer", _wrap_intArray_frompointer}, {"RNAc::new_floatP", _wrap_new_floatP}, {"RNAc::delete_floatP", _wrap_delete_floatP}, {"RNAc::floatP_getitem", _wrap_floatP_getitem}, {"RNAc::floatP_setitem", _wrap_floatP_setitem}, {"RNAc::new_floatArray", _wrap_new_floatArray}, {"RNAc::delete_floatArray", _wrap_delete_floatArray}, {"RNAc::floatArray_getitem", _wrap_floatArray_getitem}, {"RNAc::floatArray_setitem", _wrap_floatArray_setitem}, {"RNAc::floatArray_cast", _wrap_floatArray_cast}, {"RNAc::floatArray_frompointer", _wrap_floatArray_frompointer}, {"RNAc::new_doubleP", _wrap_new_doubleP}, {"RNAc::delete_doubleP", _wrap_delete_doubleP}, {"RNAc::doubleP_getitem", _wrap_doubleP_getitem}, {"RNAc::doubleP_setitem", _wrap_doubleP_setitem}, {"RNAc::new_doubleArray", _wrap_new_doubleArray}, {"RNAc::delete_doubleArray", _wrap_delete_doubleArray}, {"RNAc::doubleArray_getitem", _wrap_doubleArray_getitem}, {"RNAc::doubleArray_setitem", _wrap_doubleArray_setitem}, {"RNAc::doubleArray_cast", _wrap_doubleArray_cast}, {"RNAc::doubleArray_frompointer", _wrap_doubleArray_frompointer}, {"RNAc::new_ushortP", _wrap_new_ushortP}, {"RNAc::delete_ushortP", _wrap_delete_ushortP}, {"RNAc::ushortP_getitem", _wrap_ushortP_getitem}, {"RNAc::ushortP_setitem", _wrap_ushortP_setitem}, {"RNAc::new_shortP", _wrap_new_shortP}, {"RNAc::delete_shortP", _wrap_delete_shortP}, {"RNAc::shortP_getitem", _wrap_shortP_getitem}, {"RNAc::shortP_setitem", _wrap_shortP_setitem}, {"RNAc::cdata", _wrap_cdata}, {"RNAc::memmove", _wrap_memmove}, {"RNAc::fold", _wrap_fold}, {"RNAc::energy_of_structure", _wrap_energy_of_structure}, {"RNAc::energy_of_structure_pt", _wrap_energy_of_structure_pt}, {"RNAc::free_arrays", _wrap_free_arrays}, {"RNAc::parenthesis_structure", _wrap_parenthesis_structure}, {"RNAc::parenthesis_zuker", _wrap_parenthesis_zuker}, {"RNAc::letter_structure", _wrap_letter_structure}, {"RNAc::update_fold_params", _wrap_update_fold_params}, {"RNAc::backtrack_fold_from_pair", _wrap_backtrack_fold_from_pair}, {"RNAc::loop_energy", _wrap_loop_energy}, {"RNAc::export_fold_arrays", _wrap_export_fold_arrays}, {"RNAc::circfold", _wrap_circfold}, {"RNAc::energy_of_circ_structure", _wrap_energy_of_circ_structure}, {"RNAc::export_circfold_arrays", _wrap_export_circfold_arrays}, {"RNAc::assign_plist_from_db", _wrap_assign_plist_from_db}, {"RNAc::LoopEnergy", _wrap_LoopEnergy}, {"RNAc::HairpinE", _wrap_HairpinE}, {"RNAc::initialize_fold", _wrap_initialize_fold}, {"RNAc::energy_of_struct", _wrap_energy_of_struct}, {"RNAc::energy_of_struct_pt", _wrap_energy_of_struct_pt}, {"RNAc::energy_of_circ_struct", _wrap_energy_of_circ_struct}, {"RNAc::cofold", _wrap_cofold}, {"RNAc::free_co_arrays", _wrap_free_co_arrays}, {"RNAc::update_cofold_params", _wrap_update_cofold_params}, {"RNAc::zukersubopt", _wrap_zukersubopt}, {"RNAc::get_monomere_mfes", _wrap_get_monomere_mfes}, {"RNAc::export_cofold_arrays", _wrap_export_cofold_arrays}, {"RNAc::initialize_cofold", _wrap_initialize_cofold}, {"RNAc::pf_fold", _wrap_pf_fold}, {"RNAc::pf_circ_fold", _wrap_pf_circ_fold}, {"RNAc::pbacktrack", _wrap_pbacktrack}, {"RNAc::pbacktrack_circ", _wrap_pbacktrack_circ}, {"RNAc::free_pf_arrays", _wrap_free_pf_arrays}, {"RNAc::update_pf_params", _wrap_update_pf_params}, {"RNAc::export_bppm", _wrap_export_bppm}, {"RNAc::assign_plist_from_pr", _wrap_assign_plist_from_pr}, {"RNAc::get_pf_arrays", _wrap_get_pf_arrays}, {"RNAc::get_centroid_struct_pl", _wrap_get_centroid_struct_pl}, {"RNAc::get_centroid_struct_pr", _wrap_get_centroid_struct_pr}, {"RNAc::mean_bp_distance", _wrap_mean_bp_distance}, {"RNAc::mean_bp_distance_pr", _wrap_mean_bp_distance_pr}, {"RNAc::bppm_to_structure", _wrap_bppm_to_structure}, {"RNAc::stackProb", _wrap_stackProb}, {"RNAc::bppm_symbol", _wrap_bppm_symbol}, {"RNAc::init_pf_fold", _wrap_init_pf_fold}, {"RNAc::centroid", _wrap_centroid}, {"RNAc::mean_bp_dist", _wrap_mean_bp_dist}, {"RNAc::expLoopEnergy", _wrap_expLoopEnergy}, {"RNAc::expHairpinEnergy", _wrap_expHairpinEnergy}, {"RNAc::co_pf_fold", _wrap_co_pf_fold}, {"RNAc::free_co_pf_arrays", _wrap_free_co_pf_arrays}, {"RNAc::update_co_pf_params", _wrap_update_co_pf_params}, {"RNAc::get_concentrations", _wrap_get_concentrations}, {"RNAc::inverse_fold", _wrap_inverse_fold}, {"RNAc::inverse_pf_fold", _wrap_inverse_pf_fold}, {"RNAc::option_string", _wrap_option_string}, {"RNAc::update_alifold_params", _wrap_update_alifold_params}, {"RNAc::circalifold", _wrap_circalifold}, {"RNAc::free_alifold_arrays", _wrap_free_alifold_arrays}, {"RNAc::get_mpi", _wrap_get_mpi}, {"RNAc::readribosum", _wrap_readribosum}, {"RNAc::energy_of_alistruct", _wrap_energy_of_alistruct}, {"RNAc::encode_ali_sequence", _wrap_encode_ali_sequence}, {"RNAc::alloc_sequence_arrays", _wrap_alloc_sequence_arrays}, {"RNAc::free_sequence_arrays", _wrap_free_sequence_arrays}, {"RNAc::alipf_fold", _wrap_alipf_fold}, {"RNAc::alipf_circ_fold", _wrap_alipf_circ_fold}, {"RNAc::free_alipf_arrays", _wrap_free_alipf_arrays}, {"RNAc::alipbacktrack", _wrap_alipbacktrack}, {"RNAc::alifold", _wrap_alifold}, {"RNAc::consensus", _wrap_consensus}, {"RNAc::consens_mis", _wrap_consens_mis}, {"RNAc::COORDINATE_X_set", _wrap_COORDINATE_X_set}, {"RNAc::COORDINATE_X_get", _wrap_COORDINATE_X_get}, {"RNAc::COORDINATE_Y_set", _wrap_COORDINATE_Y_set}, {"RNAc::COORDINATE_Y_get", _wrap_COORDINATE_Y_get}, {"RNAc::COORDINATE_get", _wrap_COORDINATE_get}, {"RNAc::new_COORDINATE", _wrap_new_COORDINATE}, {"RNAc::delete_COORDINATE", _wrap_delete_COORDINATE}, {"RNAc::get_xy_coordinates", _wrap_get_xy_coordinates}, {"RNAc::SOLUTION_energy_set", _wrap_SOLUTION_energy_set}, {"RNAc::SOLUTION_energy_get", _wrap_SOLUTION_energy_get}, {"RNAc::SOLUTION_structure_set", _wrap_SOLUTION_structure_set}, {"RNAc::SOLUTION_structure_get", _wrap_SOLUTION_structure_get}, {"RNAc::SOLUTION_get", _wrap_SOLUTION_get}, {"RNAc::SOLUTION_size", _wrap_SOLUTION_size}, {"RNAc::delete_SOLUTION", _wrap_delete_SOLUTION}, {"RNAc::new_SOLUTION", _wrap_new_SOLUTION}, {"RNAc::subopt", _wrap_subopt}, {"RNAc::get_pr", _wrap_get_pr}, {"RNAc::b2HIT", _wrap_b2HIT}, {"RNAc::b2C", _wrap_b2C}, {"RNAc::b2Shapiro", _wrap_b2Shapiro}, {"RNAc::add_root", _wrap_add_root}, {"RNAc::expand_Shapiro", _wrap_expand_Shapiro}, {"RNAc::expand_Full", _wrap_expand_Full}, {"RNAc::unexpand_Full", _wrap_unexpand_Full}, {"RNAc::unweight", _wrap_unweight}, {"RNAc::unexpand_aligned_F", _wrap_unexpand_aligned_F}, {"RNAc::parse_structure", _wrap_parse_structure}, {"RNAc::make_tree", _wrap_make_tree}, {"RNAc::tree_edit_distance", _wrap_tree_edit_distance}, {"RNAc::print_tree", _wrap_print_tree}, {"RNAc::free_tree", _wrap_free_tree}, {"RNAc::Make_swString", _wrap_Make_swString}, {"RNAc::string_edit_distance", _wrap_string_edit_distance}, {"RNAc::profile_edit_distance", _wrap_profile_edit_distance}, {"RNAc::Make_bp_profile", _wrap_Make_bp_profile}, {"RNAc::Make_bp_profile_bppm", _wrap_Make_bp_profile_bppm}, {"RNAc::print_bppm", _wrap_print_bppm}, {"RNAc::free_profile", _wrap_free_profile}, {"RNAc::space", _wrap_space}, {"RNAc::xrealloc", _wrap_xrealloc}, {"RNAc::nrerror", _wrap_nrerror}, {"RNAc::warn_user", _wrap_warn_user}, {"RNAc::init_rand", _wrap_init_rand}, {"RNAc::urn", _wrap_urn}, {"RNAc::int_urn", _wrap_int_urn}, {"RNAc::filecopy", _wrap_filecopy}, {"RNAc::time_stamp", _wrap_time_stamp}, {"RNAc::random_string", _wrap_random_string}, {"RNAc::hamming", _wrap_hamming}, {"RNAc::hamming_bound", _wrap_hamming_bound}, {"RNAc::get_line", _wrap_get_line}, {"RNAc::skip_comment_lines", _wrap_skip_comment_lines}, {"RNAc::get_input_line", _wrap_get_input_line}, {"RNAc::get_multi_input_line", _wrap_get_multi_input_line}, {"RNAc::read_record", _wrap_read_record}, {"RNAc::pack_structure", _wrap_pack_structure}, {"RNAc::unpack_structure", _wrap_unpack_structure}, {"RNAc::make_pair_table", _wrap_make_pair_table}, {"RNAc::copy_pair_table", _wrap_copy_pair_table}, {"RNAc::bp_distance", _wrap_bp_distance}, {"RNAc::print_tty_input_seq", _wrap_print_tty_input_seq}, {"RNAc::print_tty_input_seq_str", _wrap_print_tty_input_seq_str}, {"RNAc::print_tty_constraint_full", _wrap_print_tty_constraint_full}, {"RNAc::print_tty_constraint", _wrap_print_tty_constraint}, {"RNAc::str_DNA2RNA", _wrap_str_DNA2RNA}, {"RNAc::str_RNA2RNA", _wrap_str_RNA2RNA}, {"RNAc::get_iindx", _wrap_get_iindx}, {"RNAc::get_indx", _wrap_get_indx}, {"RNAc::getConstraint", _wrap_getConstraint}, {"RNAc::constrain_ptypes", _wrap_constrain_ptypes}, {"RNAc::make_referenceBP_array", _wrap_make_referenceBP_array}, {"RNAc::compute_BPdifferences", _wrap_compute_BPdifferences}, {"RNAc::read_parameter_file", _wrap_read_parameter_file}, {"RNAc::write_parameter_file", _wrap_write_parameter_file}, {"RNAc::deref_any", _wrap_deref_any}, {"RNAc::scale_parameters", _wrap_scale_parameters}, {"RNAc::copy_parameters", _wrap_copy_parameters}, {"RNAc::set_parameters", _wrap_set_parameters}, {"RNAc::get_aligned_line", _wrap_get_aligned_line}, {"RNAc::make_loop_index", _wrap_make_loop_index}, {"RNAc::energy_of_move", _wrap_energy_of_move}, {"RNAc::duplexT_i_set", _wrap_duplexT_i_set}, {"RNAc::duplexT_i_get", _wrap_duplexT_i_get}, {"RNAc::duplexT_j_set", _wrap_duplexT_j_set}, {"RNAc::duplexT_j_get", _wrap_duplexT_j_get}, {"RNAc::duplexT_structure_set", _wrap_duplexT_structure_set}, {"RNAc::duplexT_structure_get", _wrap_duplexT_structure_get}, {"RNAc::duplexT_energy_set", _wrap_duplexT_energy_set}, {"RNAc::duplexT_energy_get", _wrap_duplexT_energy_get}, {"RNAc::new_duplexT", _wrap_new_duplexT}, {"RNAc::delete_duplexT", _wrap_delete_duplexT}, {"RNAc::duplexfold", _wrap_duplexfold}, {"RNAc::aliduplexfold", _wrap_aliduplexfold}, {"RNAc::encode_seq", _wrap_encode_seq}, {"RNAc::Lfold", _wrap_Lfold}, {"RNAc::aliLfold", _wrap_aliLfold}, {"RNAc::Lfoldz", _wrap_Lfoldz}, {"RNAc::PS_rna_plot", _wrap_PS_rna_plot}, {"RNAc::PS_rna_plot_a", _wrap_PS_rna_plot_a}, {"RNAc::gmlRNA", _wrap_gmlRNA}, {"RNAc::ssv_rna_plot", _wrap_ssv_rna_plot}, {"RNAc::svg_rna_plot", _wrap_svg_rna_plot}, {"RNAc::xrna_plot", _wrap_xrna_plot}, {"RNAc::PS_color_dot_plot", _wrap_PS_color_dot_plot}, {"RNAc::PS_color_dot_plot_turn", _wrap_PS_color_dot_plot_turn}, {"RNAc::PS_dot_plot_list", _wrap_PS_dot_plot_list}, {"RNAc::PS_dot_plot_turn", _wrap_PS_dot_plot_turn}, {"RNAc::PS_color_aln", _wrap_PS_color_aln}, {"RNAc::simple_xy_coordinates", _wrap_simple_xy_coordinates}, {"RNAc::PS_dot_plot", _wrap_PS_dot_plot}, {"RNAc::find_saddle", _wrap_find_saddle}, {"RNAc::get_path", _wrap_get_path}, {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 staticly 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 found, init; clientdata = clientdata; /* 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); module_head = &swig_module; } else { /* the interpreter has loaded a SWIG module, but has it loaded this one? */ found=0; iter=module_head; do { if (iter==&swig_module) { found=1; break; } iter=iter->next; } while (iter!= module_head); /* if the is found in the list, then all is done and we may leave */ if (found) return; /* otherwise we must add out module into the list */ swig_module.next = module_head->next; module_head->next = &swig_module; } /* When multiple interpeters 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 #ifdef __cplusplus extern "C" #endif XS(SWIG_init) { dXSARGS; int i; SWIG_InitializeModule(0); /* Install commands */ for (i = 0; swig_commands[i].name; i++) { newXS((char*) swig_commands[i].name,swig_commands[i].wrapper, (char*)__FILE__); } /* Install variables */ for (i = 0; swig_variables[i].name; i++) { SV *sv; sv = get_sv((char*) 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, (char *) 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((char*)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, (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_intArray, (void*) "RNA::intArray"); SWIG_TypeClientData(SWIGTYPE_p_floatArray, (void*) "RNA::floatArray"); SWIG_TypeClientData(SWIGTYPE_p_doubleArray, (void*) "RNA::doubleArray"); /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VERSION", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_double SWIG_PERL_CALL_ARGS_1((double)(0.3))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; SWIG_TypeClientData(SWIGTYPE_p_COORDINATE, (void*) "RNA::COORDINATE"); SWIG_TypeClientData(SWIGTYPE_p_SOLUTION, (void*) "RNA::SOLUTION"); /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_ERROR", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(1U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_QUIT", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(2U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_MISC", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(4U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_FASTA_HEADER", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(8U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_SEQUENCE", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(16U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_CONSTRAINT", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(32U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_NO_TRUNCATION", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(256U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_NO_REST", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(512U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_NO_SPAN", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(1024U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_NOSKIP_BLANK_LINES", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(2048U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_BLANK_LINE", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(4096U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_NOSKIP_COMMENTS", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(128U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_INPUT_COMMENT", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(8192U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_PIPE", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(1U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_DOT", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(2U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_X", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(4U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_ANG_BRACK", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(8U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_RND_BRACK", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(16U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_MULTILINE", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(32U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_NO_HEADER", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(64U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /*@SWIG:/usr/share/swig/1.3.40/perl5/perltypemaps.swg,65,%set_constant@*/ do { SV *sv = get_sv((char*) SWIG_prefix "VRNA_CONSTRAINT_ALL", TRUE | 0x2 | GV_ADDMULTI); sv_setsv(sv, SWIG_From_unsigned_SS_int SWIG_PERL_CALL_ARGS_1((unsigned int)(128U))); SvREADONLY_on(sv); } while(0) /*@SWIG@*/; /* work around segfault when script tries to free symbolset */ symbolset = (char *) space(21); strcpy(symbolset, "AUGC"); SWIG_TypeClientData(SWIGTYPE_p_duplexT, (void*) "RNA::duplexT"); ST(0) = &PL_sv_yes; XSRETURN(1); }