static double expShulen(double T, /* absolute error */
double M, /* min logarithm */
double d,
double p,
GtUword subjectLength,
double *ln_n_fac,
double *s1,
GtUword n_s)
{
GtUword i;
int thresholdReached = 0;
double prob_i, probOld, delta, factor;
double e = 0.0; /* expectation */
double t = 1.0 - d;
double p_t = t;
probOld = 0.0;
/*since for i = 0, the whole expression is 0*/
for (i = 1LU; i < subjectLength; i++) {
factor = 1.0 - p_t;
if (!thresholdReached) {
prob_i = factor * pmax(M, i, p,
subjectLength,
&thresholdReached,
ln_n_fac,
s1,
n_s);
}
else
prob_i = factor; /* prob_i = factor * s, where s = 1 */
delta = (prob_i - probOld) * i; /* delta should always be positive */
gt_assert(gt_double_equals_double(delta, 0.0) ||
gt_double_larger_double(delta, 0.0));
e += delta; /* expectation of avg shulen length(Q, S) */
/* check error */
if (1.0 <= e && delta / e <= T)
break;
p_t *= t;
probOld = prob_i;
}
return e;
}
void gt_firstcodes_spacelog_add(GtFirstcodesspacelog *fcsl,
int line,
const char *filename,
bool add,
const char *title,
bool work,
size_t size)
{
GtFirstcodespacelogentry *entry;
size_t logspace;
if (add)
{
entry = gt_spacelog_find(fcsl,title);
if (entry != NULL)
{
if (entry->size != 0)
{
fprintf(stderr,"existing entry for title \"%s\""
"(from file %s, line %d) "
"in spacelog entries must have size 0\n",
title,filename,line);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_spacelog_updateaddentry(entry,filename,line,title,size,work);
} else
{
gt_spacelog_addentry(fcsl,filename,line,title,size,work);
}
if (work)
{
fcsl->workspace += size;
} else
{
fcsl->splitspace += size;
}
gt_firstcodes_updatemax(fcsl);
} else
{
entry = gt_spacelog_find(fcsl,title);
if (entry == NULL)
{
fprintf(stderr,"cannot find title \"%s\" (from file %s, line %d) "
"in spacelog entries\n",title,filename,line);
(void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if ((entry->work && !work) || (!entry->work && work))
{
fprintf(stderr,"for title \"%s\" (from file %s, line %d) "
"in spacelog entries: inconsistent work/splitassignment\n",
title,filename,line);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (work)
{
if (entry->size > fcsl->workspace)
{
gt_firstcodes_subtract_error(title, filename, line, entry->size, true,
fcsl->workspace);
(void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
fcsl->workspace -= entry->size;
} else
{
if (entry->size > fcsl->splitspace)
{
gt_firstcodes_subtract_error(title, filename, line, entry->size, false,
fcsl->splitspace);
(void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
fcsl->splitspace -= entry->size;
}
if (size > 0)
{
gt_spacelog_updateaddentry(entry,filename,line,title,size,work);
if (work)
{
fcsl->workspace += size;
} else
{
fcsl->splitspace += size;
}
gt_firstcodes_updatemax(fcsl);
if (size > entry->size)
{
add = true;
size -= entry->size;
} else
{
size = entry->size - size;
}
} else
{
size = entry->size;
entry->size = 0;
}
}
logspace = fcsl->workspace+fcsl->splitspace;
gt_log_log(
#ifdef SKDEBUG
"file %s, line %d: "
#endif
"%s %s= %.2f, %s, w=%.2f, s=%.2f, sum=%.2f MB",
#ifdef SKDEBUG
filename,
line,
#endif
work ? "w" : "s",
add ? "+" : "-",
GT_MEGABYTES(size),
title,
GT_MEGABYTES(fcsl->workspace),
GT_MEGABYTES(fcsl->splitspace),
GT_MEGABYTES(logspace));
#ifdef SKDEBUG
if (gt_ma_bookkeeping_enabled())
{
unsigned long realspace = gt_ma_get_space_current() +
gt_fa_get_space_current();
gt_log_log("current space usage %.2f MB (%.2f+%.2f)",
GT_MEGABYTES(realspace),
GT_MEGABYTES(gt_ma_get_space_current()),
GT_MEGABYTES(gt_fa_get_space_current()));
if (fcsl->calc_difference)
{
double percent_difference;
if ((unsigned long) logspace > realspace)
{
fprintf(stderr,"overestimating logspace\n");
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (realspace >= 1000000UL)
{
/*
printf("realspace=%lu,logspace=%lu\n",realspace,
(unsigned long) logspace);
*/
percent_difference = 100.0 * (double) (realspace - logspace)/realspace;
if (gt_double_larger_double(percent_difference,3.0))
{
fprintf(stderr,"space difference of %.2f%% is too large\n",
percent_difference);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (gt_double_smaller_double(fcsl->max_percent_difference,
percent_difference))
{
fcsl->max_percent_difference = percent_difference;
}
}
}
}
#endif
}
