bool gt_lcpintervalfindcharchildintv_simple(const GtEncseq *encseq,
GtReadmode readmode,
GtUword totallength,
const ESASuffixptr *suftab,
Simplelcpinterval *itv,
GtUchar cc,
GtUword offset,
GtUword left,
GtUword right)
{
GtUword pos;
pos = ESASUFFIXPTRGET(suftab,left) + offset;
if (cc < SEQUENCE(encseq,pos))
{
return false;
}
pos = ESASUFFIXPTRGET(suftab,right) + offset;
if (cc > SEQUENCE(encseq,pos))
{
return false;
}
itv->left = lcpintervalfindfirst(encseq,
readmode,
totallength,
suftab,
cc,
offset,
left,
right);
if (itv->left == ULONG_MAX)
{
return false;
}
itv->right = lcpintervalfindlast(encseq,
readmode,
totallength,
suftab,
cc,
offset,
itv->left + 1,
right);
if (itv->right == ULONG_MAX)
{
itv->right = itv->left;
}
return true;
}
static GtUword lcpintervalfindlast(const GtEncseq *encseq,
GtReadmode readmode,
GtUword totallength,
const ESASuffixptr *suftab,
GtUchar cc,
GtUword offset,
GtUword left,
GtUword right)
{
GtUword found = ULONG_MAX;
while (left <= right)
{
GtUword mid = left + GT_DIV2(right - left + 1);
GtUword pos = ESASUFFIXPTRGET(suftab,mid) + offset;
GtUchar midcc = SEQUENCE(encseq,pos);
if (cc < midcc)
{
if (mid == 0)
{
break;
}
right = mid - 1;
} else
{
if (cc == midcc)
{
found = mid;
}
left = mid + 1;
}
}
return found;
}
static unsigned long lcpintervalfindrightbound(const GtEncseq *encseq,
GtReadmode readmode,
unsigned long totallength,
const ESASuffixptr *suftab,
GtUchar cc,
unsigned long offset,
unsigned long left,
unsigned long right)
{
unsigned long pos, mid;
GtUchar midcc;
while (right > left+1)
{
mid = GT_DIV2(left+right);
pos = ESASUFFIXPTRGET(suftab,mid) + offset;
midcc = SEQUENCE(encseq,pos);
if (cc < midcc)
{
right = mid;
} else
{
left = mid;
}
}
return left;
}
bool gt_lcpintervalfindcharchildintv(const GtEncseq *encseq,
GtReadmode readmode,
unsigned long totallength,
const ESASuffixptr *suftab,
Simplelcpinterval *itv,
GtUchar cc,
unsigned long offset,
unsigned long left,
unsigned long right)
{
GtUchar leftcc, rightcc;
unsigned long pos, rightbound, leftbound = left;
pos = ESASUFFIXPTRGET(suftab,right) + offset;
rightcc = SEQUENCE(encseq,pos);
while (true)
{
pos = ESASUFFIXPTRGET(suftab,leftbound) + offset;
leftcc = SEQUENCE(encseq,pos);
if (leftcc == rightcc)
{
break;
}
rightbound = lcpintervalfindrightbound(encseq,readmode,
totallength,suftab,leftcc,
offset,leftbound,right);
if (leftcc == cc)
{
itv->left = leftbound;
itv->right = rightbound;
return true;
}
if (leftcc > cc)
{
return false;
}
leftbound = rightbound+1;
}
if (leftcc == cc)
{
itv->left = leftbound;
itv->right = right;
return true;
}
return false;
}
void gt_lcpintervalsplitwithoutspecial(GtArrayBoundswithchar *bwci,
const GtEncseq *encseq,
GtReadmode readmode,
unsigned long totallength,
const ESASuffixptr *suftab,
unsigned long parentoffset,
unsigned long parentleft,
unsigned long parentright)
{
GtUchar leftcc, rightcc;
unsigned long rightbound = 0, leftbound = parentleft;
/* call gt_lcpintervalextendlcp and verify if interval can be extended by
some character */
bwci->nextfreeBoundswithchar = 0;
rightcc = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentright) + parentoffset);
while (true)
{
leftcc = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,leftbound) + parentoffset);
gt_assert(bwci->nextfreeBoundswithchar < bwci->allocatedBoundswithchar);
if (ISSPECIAL(leftcc))
{
ADDPREVIOUSRBOUND(rightbound);
ADDCURRENTLBOUND(rightbound+1);
return;
}
ADDPREVIOUSRBOUND(leftbound-1);
ADDCURRENTLBOUND(leftbound);
ADDCURRENTINCHAR(leftcc);
if (leftcc == rightcc)
{
break;
}
rightbound = lcpintervalfindrightbound(encseq,readmode,totallength,suftab,
leftcc,parentoffset,
leftbound,parentright);
leftbound = rightbound+1;
}
gt_assert(bwci->nextfreeBoundswithchar < bwci->allocatedBoundswithchar);
ADDPREVIOUSRBOUND(parentright);
ADDCURRENTLBOUND(parentright+1);
}
GtUchar gt_lcpintervalextendlcp(const GtEncseq *encseq,
GtReadmode readmode,
const ESASuffixptr *suftab,
unsigned long totallength,
GtUchar alphasize,
unsigned long parentoffset,
unsigned long parentleft,
unsigned long parentright)
{
GtUchar ccl, ccr;
ccl = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentleft) + parentoffset);
ccr = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentright) + parentoffset);
if (ccl != ccr || ISSPECIAL(ccl))
{
return alphasize;
}
gt_assert(ccl < alphasize);
return ccl;
}
main(int ac, char **av)
{
int i;
FILE *ifp;
char line[LINE_SIZE];
prog = av[0];
flt_scale = (double)1.0;
flags = 0;
d_path = NULL;
process_options(ac, av);
if (flags & VERBOSE)
fprintf(ofp,
"-- TPC %s Parameter Substitution (Version %d.%d.%d%s)\n",
NAME, VERSION, RELEASE, MODIFICATION, PATCH);
setup();
if (!(flags & DFLT)) /* perturb the RNG */
{
if (!(flags & SEED))
rndm = (long)((unsigned)time(NULL) * DSS_PROC);
if (rndm < 0)
rndm += 2147483647;
Seed[0].value = rndm;
for (i=1; i <= QUERIES_PER_SET; i++)
{
Seed[0].value = NextRand(Seed[0].value);
Seed[i].value = Seed[0].value;
}
printf("-- using %ld as a seed to the RNG\n", rndm);
}
else
printf("-- using default substitutions\n");
if (flags & INIT) /* init stream with ifile */
{
ifp = fopen(ifile, "r");
OPEN_CHECK(ifp, ifile);
while (fgets(line, LINE_SIZE, ifp) != NULL)
fprintf(stdout, "%s", line);
}
if (snum >= 0)
if (optind < ac)
for (i=optind; i < ac; i++)
{
char qname[10];
sprintf(qname, "%d", SEQUENCE(snum, atoi(av[i])));
qsub(qname, flags);
}
else
for (i=1; i <= QUERIES_PER_SET; i++)
{
char qname[10];
sprintf(qname, "%d", SEQUENCE(snum, i));
qsub(qname, flags);
}
else
if (optind < ac)
for (i=optind; i < ac; i++)
qsub(av[i], flags);
else
for (i=1; i <= QUERIES_PER_SET; i++)
{
char qname[10];
sprintf(qname, "%d", i);
qsub(qname, flags);
}
if (flags & TERMINATE) /* terminate stream with tfile */
{
ifp = fopen(tfile, "r");
if (ifp == NULL)
OPEN_CHECK(ifp, tfile);
while (fgets(line, LINE_SIZE, ifp) != NULL)
fprintf(stdout, "%s", line);
}
return(0);
}
