static void testmulticharactercompare(const Encodedsequence *encseq,
Readmode readmode,
unsigned long multicharcmptrials)
{
Encodedsequencescanstate *esr1, *esr2;
Seqpos pos1, pos2, totallength;
unsigned long trial;
bool fwd = ISDIRREVERSE(readmode) ? false : true,
complement = ISDIRCOMPLEMENT(readmode) ? true : false;
esr1 = newEncodedsequencescanstate();
esr2 = newEncodedsequencescanstate();
totallength = getencseqtotallength(encseq);
srand48(42349421);
(void) multicharactercompare_withtest(encseq,fwd,complement,esr1,0,esr2,0);
(void) multicharactercompare_withtest(encseq,fwd,complement,esr1,0,esr2,
totallength-1);
(void) multicharactercompare_withtest(encseq,fwd,complement,esr1,
totallength-1,esr2,0);
(void) multicharactercompare_withtest(encseq,fwd,complement,esr1,
totallength-1,esr2,totallength-1);
for (trial = 0; trial < multicharcmptrials; trial++)
{
pos1 = (Seqpos) (drand48() * (double) totallength);
pos2 = (Seqpos) (drand48() * (double) totallength);
(void) multicharactercompare_withtest(encseq,fwd,complement,
esr1,pos1,esr2,pos2);
}
freeEncodedsequencescanstate(&esr1);
freeEncodedsequencescanstate(&esr2);
}
int testencodedsequence(const GtStrArray *filenametab,
const Encodedsequence *encseq,
Readmode readmode,
unsigned long scantrials,
unsigned long multicharcmptrials,
GtError *err)
{
bool fwd = ISDIRREVERSE(readmode) ? false : true,
complement = ISDIRCOMPLEMENT(readmode) ? true : false;
if (hasfastspecialrangeenumerator(encseq))
{
checkextractunitatpos(encseq,fwd,complement);
if (multicharcmptrials > 0)
{
testmulticharactercompare(encseq,readmode,multicharcmptrials);
}
}
if (!complement)
{
checkextractspecialbits(encseq,fwd);
}
if (scantrials > 0)
{
testscanatpos(encseq,readmode,scantrials);
}
return testfullscan(filenametab,encseq,readmode,err);
}
static Seqpos *leftcontextofspecialchardist(unsigned int numofchars,
const Encodedsequence *encseq,
Readmode readmode)
{
GtUchar cc;
unsigned int idx;
Seqpos *specialchardist, totallength = getencseqtotallength(encseq);
specialchardist = gt_malloc(sizeof(*specialchardist) * numofchars);
for (idx = 0; idx<numofchars; idx++)
{
specialchardist[idx] = 0;
}
if (hasspecialranges(encseq))
{
Specialrangeiterator *sri;
Sequencerange range;
sri = newspecialrangeiterator(encseq,true);
if (ISDIRREVERSE(readmode))
{
Readmode thismode = (readmode == Reversemode) ? Forwardmode
: Complementmode;
while (nextspecialrangeiterator(&range,sri))
{
if (range.rightpos < totallength)
{
cc = getencodedchar(encseq,range.rightpos,thismode);
if (ISNOTSPECIAL(cc))
{
specialchardist[cc]++;
}
}
}
} else
{
while (nextspecialrangeiterator(&range,sri))
{
gt_assert(range.leftpos < totallength);
if (range.leftpos > 0)
{
cc = getencodedchar(encseq,range.leftpos-1,readmode);
if (ISNOTSPECIAL(cc))
{
specialchardist[cc]++;
}
}
}
}
freespecialrangeiterator(&sri);
}
if (getencseqlengthofspecialsuffix(encseq) == 0)
{
cc = getencodedchar(encseq,totallength-1,readmode);
gt_assert(ISNOTSPECIAL(cc));
specialchardist[cc]++;
}
return specialchardist;
}
void gt_copysortsuffixes(const GtBucketspec2 *bucketspec2,
Seqpos *suftab,
Verboseinfo *verboseinfo)
{
Seqpos hardwork = 0, **targetptr;
unsigned int idx, idxsource, source, second;
#ifdef WITHSUFFIXES
{
const Seqpos *ptr;
for (ptr = suftab; ptr < suftab + bucketspec2->partwidth; ptr++)
{
showsequenceatstartpos(stdout,
ISDIRREVERSE(readmode) ? false : true,
ISDIRCOMPLEMENT(readmode) ? true : false,
encseq,
*ptr);
}
}
#endif
targetptr = gt_malloc(sizeof(*targetptr) * bucketspec2->numofchars);
for (idxsource = 0; idxsource<bucketspec2->numofchars; idxsource++)
{
source = bucketspec2->order[idxsource];
for (second = 0; second < bucketspec2->numofchars; second++)
{
if (!bucketspec2->subbuckettab[source][second].sorted && source != second)
{
gt_assert(bucketspec2->subbuckettab[source][second].hardworktodo);
showverbose(verboseinfo,"hard work for %u %u",source,second);
hardwork += getendidx(bucketspec2,source,second) -
getstartidx(bucketspec2,source,second);
bucketspec2->subbuckettab[source][second].sorted = true;
} else
{
gt_assert(!bucketspec2->subbuckettab[source][second].hardworktodo);
}
}
if (getstartidx(bucketspec2,source,0) <
getstartidx(bucketspec2,source,source))
{
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
targetptr[idx] = suftab + getstartidx(bucketspec2,idx,source);
}
forwardderive(bucketspec2,
targetptr,
source,
suftab + getstartidx(bucketspec2,source,0));
}
if (getendidx(bucketspec2,source,source) <
getendidx(bucketspec2,source,bucketspec2->numofchars))
{
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
targetptr[idx] = suftab + getendidx(bucketspec2,idx,source) - 1;
}
backwardderive(bucketspec2,
targetptr,
source,
suftab +
getendidx(bucketspec2,source,bucketspec2->numofchars) - 1);
}
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
bucketspec2->subbuckettab[idx][source].sorted = true;
}
bucketspec2->superbuckettab[source].sorted = true;
}
gt_free(targetptr);
showverbose(verboseinfo,"hardwork = " FormatSeqpos " (%.2f)",
PRINTSeqposcast(hardwork),
(double) hardwork/getencseqtotallength(bucketspec2->encseq));
}
