static void fpe_reset(Sigfunc *handler)
{
/* Reset the exception handling machinery, and reset the signal
* handler for SIGFPE to the given handler.
*/
/*-- IRIX -----------------------------------------------------------------*/
#if defined(sgi)
/* See man page on handle_sigfpes -- must link with -lfpe
* My usage doesn't follow the man page exactly. Maybe somebody
* else can explain handle_sigfpes to me....
* cc -c -I/usr/local/python/include fpectlmodule.c
* ld -shared -o fpectlmodule.so fpectlmodule.o -lfpe
*/
#include <sigfpe.h>
typedef void user_routine (unsigned[5], int[2]);
typedef void abort_routine (unsigned long);
handle_sigfpes(_OFF, 0,
(user_routine *)0,
_TURN_OFF_HANDLER_ON_ERROR,
NULL);
handle_sigfpes(_ON, _EN_OVERFL | _EN_DIVZERO | _EN_INVALID,
(user_routine *)0,
_ABORT_ON_ERROR,
NULL);
PyOS_setsig(SIGFPE, handler);
/*-- SunOS and Solaris ----------------------------------------------------*/
#elif defined(sun)
/* References: ieee_handler, ieee_sun, ieee_functions, and ieee_flags
man pages (SunOS or Solaris)
cc -c -I/usr/local/python/include fpectlmodule.c
ld -G -o fpectlmodule.so -L/opt/SUNWspro/lib fpectlmodule.o -lsunmath -lm
*/
#include <math.h>
#ifndef _SUNMATH_H
extern void nonstandard_arithmetic(void);
extern int ieee_flags(const char*, const char*, const char*, char **);
extern long ieee_handler(const char*, const char*, sigfpe_handler_type);
#endif
char *mode="exception", *in="all", *out;
(void) nonstandard_arithmetic();
(void) ieee_flags("clearall",mode,in,&out);
(void) ieee_handler("set","common",(sigfpe_handler_type)handler);
PyOS_setsig(SIGFPE, handler);
/*-- HPUX -----------------------------------------------------------------*/
#elif defined(__hppa) || defined(hppa)
/* References: fpsetmask man page */
/* cc -Aa +z -c -I/usr/local/python/include fpectlmodule.c */
/* ld -b -o fpectlmodule.sl fpectlmodule.o -lm */
#include <math.h>
fpsetdefaults();
PyOS_setsig(SIGFPE, handler);
/*-- IBM AIX --------------------------------------------------------------*/
#elif defined(__AIX) || defined(_AIX)
/* References: fp_trap, fp_enable man pages */
#include <fptrap.h>
fp_trap(FP_TRAP_SYNC);
fp_enable(TRP_INVALID | TRP_DIV_BY_ZERO | TRP_OVERFLOW);
PyOS_setsig(SIGFPE, handler);
/*-- DEC ALPHA OSF --------------------------------------------------------*/
#elif defined(__alpha) && defined(__osf__)
/* References: exception_intro, ieee man pages */
/* cc -c -I/usr/local/python/include fpectlmodule.c */
/* ld -shared -o fpectlmodule.so fpectlmodule.o */
#include <machine/fpu.h>
unsigned long fp_control =
IEEE_TRAP_ENABLE_INV | IEEE_TRAP_ENABLE_DZE | IEEE_TRAP_ENABLE_OVF;
ieee_set_fp_control(fp_control);
PyOS_setsig(SIGFPE, handler);
/*-- DEC ALPHA LINUX ------------------------------------------------------*/
#elif defined(__alpha) && defined(linux)
#include <asm/fpu.h>
unsigned long fp_control =
IEEE_TRAP_ENABLE_INV | IEEE_TRAP_ENABLE_DZE | IEEE_TRAP_ENABLE_OVF;
ieee_set_fp_control(fp_control);
PyOS_setsig(SIGFPE, handler);
/*-- DEC ALPHA VMS --------------------------------------------------------*/
#elif defined(__ALPHA) && defined(__VMS)
IEEE clrmsk;
IEEE setmsk;
clrmsk.ieee$q_flags =
IEEE$M_TRAP_ENABLE_UNF | IEEE$M_TRAP_ENABLE_INE |
IEEE$M_MAP_UMZ;
setmsk.ieee$q_flags =
IEEE$M_TRAP_ENABLE_INV | IEEE$M_TRAP_ENABLE_DZE |
IEEE$M_TRAP_ENABLE_OVF;
sys$ieee_set_fp_control(&clrmsk, &setmsk, 0);
PyOS_setsig(SIGFPE, handler);
/*-- HP IA64 VMS --------------------------------------------------------*/
#elif defined(__ia64) && defined(__VMS)
PyOS_setsig(SIGFPE, handler);
/*-- Cray Unicos ----------------------------------------------------------*/
#elif defined(cray)
/* UNICOS delivers SIGFPE by default, but no matherr */
#ifdef HAS_LIBMSET
libmset(-1);
#endif
PyOS_setsig(SIGFPE, handler);
/*-- FreeBSD ----------------------------------------------------------------*/
#elif defined(__FreeBSD__)
fpresetsticky(fpgetsticky());
fpsetmask(FP_X_INV | FP_X_DZ | FP_X_OFL);
PyOS_setsig(SIGFPE, handler);
/*-- Linux ----------------------------------------------------------------*/
#elif defined(linux)
#ifdef __GLIBC__
#include <fpu_control.h>
#else
#include <i386/fpu_control.h>
#endif
#ifdef _FPU_SETCW
{
fpu_control_t cw = 0x1372;
_FPU_SETCW(cw);
}
#else
__setfpucw(0x1372);
#endif
PyOS_setsig(SIGFPE, handler);
/*-- Microsoft Windows, NT ------------------------------------------------*/
#elif defined(_MSC_VER)
/* Reference: Visual C++ Books Online 4.2,
Run-Time Library Reference, _control87, _controlfp */
#include <float.h>
unsigned int cw = _EM_INVALID | _EM_ZERODIVIDE | _EM_OVERFLOW;
(void)_controlfp(0, cw);
PyOS_setsig(SIGFPE, handler);
/*-- Give Up --------------------------------------------------------------*/
#else
fputs("Operation not implemented\n", stderr);
#endif
}
static void fpe_reset(Sigfunc *handler)
{
/* Reset the exception handling machinery, and reset the signal
* handler for SIGFPE to the given handler.
*/
/*-- SunOS and Solaris ----------------------------------------------------*/
#if defined(sun)
/* References: ieee_handler, ieee_sun, ieee_functions, and ieee_flags
man pages (SunOS or Solaris)
cc -c -I/usr/local/python/include fpectlmodule.c
ld -G -o fpectlmodule.so -L/opt/SUNWspro/lib fpectlmodule.o -lsunmath -lm
*/
#include <math.h>
#ifndef _SUNMATH_H
extern void nonstandard_arithmetic(void);
extern int ieee_flags(const char*, const char*, const char*, char **);
extern long ieee_handler(const char*, const char*, sigfpe_handler_type);
#endif
char *mode="exception", *in="all", *out;
(void) nonstandard_arithmetic();
(void) ieee_flags("clearall",mode,in,&out);
(void) ieee_handler("set","common",(sigfpe_handler_type)handler);
PyOS_setsig(SIGFPE, handler);
/*-- HPUX -----------------------------------------------------------------*/
#elif defined(__hppa) || defined(hppa)
/* References: fpsetmask man page */
/* cc -Aa +z -c -I/usr/local/python/include fpectlmodule.c */
/* ld -b -o fpectlmodule.sl fpectlmodule.o -lm */
#include <math.h>
fpsetdefaults();
PyOS_setsig(SIGFPE, handler);
/*-- IBM AIX --------------------------------------------------------------*/
#elif defined(__AIX) || defined(_AIX)
/* References: fp_trap, fp_enable man pages */
#include <fptrap.h>
fp_trap(FP_TRAP_SYNC);
fp_enable(TRP_INVALID | TRP_DIV_BY_ZERO | TRP_OVERFLOW);
PyOS_setsig(SIGFPE, handler);
/*-- DEC ALPHA LINUX ------------------------------------------------------*/
#elif defined(__alpha) && defined(linux)
#include <asm/fpu.h>
unsigned long fp_control =
IEEE_TRAP_ENABLE_INV | IEEE_TRAP_ENABLE_DZE | IEEE_TRAP_ENABLE_OVF;
ieee_set_fp_control(fp_control);
PyOS_setsig(SIGFPE, handler);
/*-- Cray Unicos ----------------------------------------------------------*/
#elif defined(cray)
/* UNICOS delivers SIGFPE by default, but no matherr */
#ifdef HAS_LIBMSET
libmset(-1);
#endif
PyOS_setsig(SIGFPE, handler);
/*-- FreeBSD ----------------------------------------------------------------*/
#elif defined(__FreeBSD__)
fpresetsticky(fpgetsticky());
fpsetmask(FP_X_INV | FP_X_DZ | FP_X_OFL);
PyOS_setsig(SIGFPE, handler);
/*-- Linux ----------------------------------------------------------------*/
#elif defined(linux)
#ifdef __GLIBC__
#include <fpu_control.h>
#else
#include <i386/fpu_control.h>
#endif
#ifdef _FPU_SETCW
{
fpu_control_t cw = 0x1372;
_FPU_SETCW(cw);
}
#else
__setfpucw(0x1372);
#endif
PyOS_setsig(SIGFPE, handler);
/*-- Microsoft Windows, NT ------------------------------------------------*/
#elif defined(_MSC_VER)
/* Reference: Visual C++ Books Online 4.2,
Run-Time Library Reference, _control87, _controlfp */
#include <float.h>
unsigned int cw = _EM_INVALID | _EM_ZERODIVIDE | _EM_OVERFLOW;
(void)_controlfp(0, cw);
PyOS_setsig(SIGFPE, handler);
/*-- Give Up --------------------------------------------------------------*/
#else
fputs("Operation not implemented\n", stderr);
#endif
}
PUBLIC float
vrna_pf(vrna_fold_compound_t *vc,
char *structure){
int n;
FLT_OR_DBL Q;
double free_energy;
vrna_md_t *md;
vrna_exp_param_t *params;
vrna_mx_pf_t *matrices;
free_energy = (float)(INF/100.);
if(vc){
/* make sure, everything is set up properly to start partition function computations */
if(!vrna_fold_compound_prepare(vc, VRNA_OPTION_PF)){
vrna_message_warning("vrna_pf@part_func.c: Failed to prepare vrna_fold_compound");
return free_energy;
}
n = vc->length;
params = vc->exp_params;
matrices = vc->exp_matrices;
md = &(params->model_details);
#ifdef _OPENMP
/* Explicitly turn off dynamic threads */
omp_set_dynamic(0);
#endif
#ifdef SUN4
nonstandard_arithmetic();
#else
#ifdef HP9
fpsetfastmode(1);
#endif
#endif
/* call user-defined recursion status callback function */
if(vc->stat_cb)
vc->stat_cb(VRNA_STATUS_PF_PRE, vc->auxdata);
switch(vc->type){
case VRNA_FC_TYPE_SINGLE: /* do the linear pf fold and fill all matrices */
pf_linear(vc);
if(md->circ)
pf_circ(vc); /* do post processing step for circular RNAs */
break;
case VRNA_FC_TYPE_COMPARATIVE: /* do the linear pf fold and fill all matrices */
alipf_linear(vc);
/* calculate post processing step for circular */
/* RNAs */
if(md->circ)
wrap_alipf_circ(vc, structure);
break;
default: vrna_message_warning("vrna_pf@part_func.c: Unrecognized fold compound type");
return free_energy;
break;
}
/* call user-defined recursion status callback function */
if(vc->stat_cb)
vc->stat_cb(VRNA_STATUS_PF_POST, vc->auxdata);
/* calculate base pairing probability matrix (bppm) */
if(md->compute_bpp){
vrna_pairing_probs(vc, structure);
#ifdef VRNA_BACKWARD_COMPAT
/*
* Backward compatibility:
* This block may be removed if deprecated functions
* relying on the global variable "pr" vanish from within the package!
*/
pr = matrices->probs;
/*
{
if(pr) free(pr);
pr = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));
memcpy(pr, probs, sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));
}
*/
#endif
}
if (md->backtrack_type=='C')
Q = matrices->qb[vc->iindx[1]-n];
else if (md->backtrack_type=='M')
Q = matrices->qm[vc->iindx[1]-n];
else Q = (md->circ) ? matrices->qo : matrices->q[vc->iindx[1]-n];
/* ensemble free energy in Kcal/mol */
if (Q<=FLT_MIN)
vrna_message_warning("pf_scale too large");
switch(vc->type){
case VRNA_FC_TYPE_COMPARATIVE: free_energy = (-log(Q)-n*log(params->pf_scale))*params->kT/(1000.0 * vc->n_seq);
break;
case VRNA_FC_TYPE_SINGLE: /* fall through */
default: free_energy = (-log(Q)-n*log(params->pf_scale))*params->kT/1000.0;
break;
}
#ifdef SUN4
standard_arithmetic();
#else
#ifdef HP9
fpsetfastmode(0);
#endif
#endif
}
return free_energy;
}
