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;
}
static void runscanatpostrial(const Encodedsequence *encseq,
Encodedsequencescanstate *esr,
Readmode readmode,Seqpos startpos)
{
Seqpos pos, totallength;
GtUchar ccra, ccsr;
totallength = getencseqtotallength(encseq);
initEncodedsequencescanstate(esr,encseq,readmode,startpos);
for (pos=startpos; pos < totallength; pos++)
{
ccra = getencodedchar(encseq,pos,readmode); /* Random access */
ccsr = sequentialgetencodedchar(encseq,esr,pos,readmode);
if (ccra != ccsr)
{
fprintf(stderr,"startpos = " FormatSeqpos
" access=%s, mode=%s: position=" FormatSeqpos
": random access (correct) = %u != %u = "
" sequential read (wrong)\n",
PRINTSeqposcast(startpos),
encseqaccessname(encseq),
showreadmode(readmode),
PRINTSeqposcast(pos),
(unsigned int) ccra,
(unsigned int) ccsr);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
}
}
static void forwardderive(const GtBucketspec2 *bucketspec2,
Seqpos **targetptr,
unsigned int source,
Seqpos *idx)
{
Seqpos startpos;
GtUchar cc;
gt_assert (idx < targetptr[source]);
for (; idx < targetptr[source]; idx++)
{
startpos = *idx;
if (startpos > 0)
{
cc = getencodedchar(bucketspec2->encseq,startpos-1,bucketspec2->readmode);
/*printf("fwd: superbucket[%u].sorted = %s\n",(unsigned int) cc,
bucketspec2->superbuckettab[cc].sorted ? "true" :
"false"); */
if (ISNOTSPECIAL(cc) && !bucketspec2->superbuckettab[cc].sorted)
{
*(targetptr[cc]) = startpos - 1;
targetptr[cc]++;
}
}
}
}
unsigned long distanceofshortstringsencseq(unsigned long *eqsvector,
unsigned int alphasize,
const GtUchar *useq,
unsigned long ulen,
const Encodedsequence *encseq,
Seqpos vstartpos,
Seqpos vlen)
{
DECLARELOCALVARS;
GtUchar cc;
Seqpos pos;
initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
for (pos = vstartpos; pos < vstartpos + vlen; pos++)
{
cc = getencodedchar(encseq,pos,Forwardmode);
COMPUTENEWDIST(cc);
}
return distval;
}
static void backwardderive(const GtBucketspec2 *bucketspec2,
Seqpos **targetptr,
unsigned int source,
Seqpos *idx)
{
Seqpos startpos;
GtUchar cc;
gt_assert (idx > targetptr[source]);
for (; idx > targetptr[source]; idx--)
{
startpos = *idx;
if (startpos > 0)
{
cc = getencodedchar(bucketspec2->encseq,startpos-1,bucketspec2->readmode);
/*printf("back: superbucket[%u].sorted = %s\n",(unsigned int) cc,
bucketspec2->superbuckettab[cc].sorted ? "true" :
"false");*/
if (ISNOTSPECIAL(cc) && !bucketspec2->superbuckettab[cc].sorted)
{
/*
if (suftab[targetptr[cc]] != startpos - 1)
{
fprintf(stderr,"targetptr[%u]=%lu: suftab = %lu != "
"%lu = startpos - 1\n",
cc,
(unsigned long) targetptr[cc],
(unsigned long) suftab[targetptr[cc]],
(unsigned long) (startpos-1));
exit(EXIT_FAILURE);
}
*/
*(targetptr[cc]) = startpos - 1;
targetptr[cc]--;
}
}
}
}
Definedunsignedlong forwardprefixmatch(const Encodedsequence *encseq,
unsigned int alphasize,
Seqpos startpos,
bool nowildcards,
unsigned long *eqsvector,
const GtUchar *useq,
unsigned long ulen,
unsigned long maxdistance)
{
DECLARELOCALVARS;
Seqpos pos, totallength = getencseqtotallength(encseq);
GtUchar cc;
Definedunsignedlong result;
initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
gt_assert(maxdistance > 0);
for (pos = startpos; /* Nothing */; pos++)
{
gt_assert(pos - startpos <= (Seqpos) (ulen + maxdistance));
cc = getencodedchar(encseq,pos,Forwardmode);
if (nowildcards && cc == (GtUchar) WILDCARD)
{
result.defined = false;
result.valueunsignedlong = 0;
return result;
}
COMPUTENEWDIST(cc);
if (distval <= maxdistance || pos == totallength-1)
{
break;
}
}
result.defined = true;
result.valueunsignedlong = (unsigned long) (pos - startpos + 1);
return result;
}
static int testfullscan(const GtStrArray *filenametab,
const Encodedsequence *encseq,
Readmode readmode,
GtError *err)
{
Seqpos pos, totallength;
GtUchar ccscan = 0, ccra, ccsr;
GtSequenceBuffer *fb = NULL;
int retval;
bool haserr = false;
Encodedsequencescanstate *esr;
unsigned long long fullscanpbar = 0;
gt_error_check(err);
totallength = getencseqtotallength(encseq);
gt_progressbar_start(&fullscanpbar,(unsigned long long) totallength);
if (filenametab != NULL)
{
fb = gt_sequence_buffer_new_guess_type((GtStrArray*) filenametab, err);
if (!fb)
haserr = true;
if (!haserr)
gt_sequence_buffer_set_symbolmap(fb, getencseqAlphabetsymbolmap(encseq));
}
if (!haserr) {
esr = newEncodedsequencescanstate();
initEncodedsequencescanstate(esr,encseq,readmode,0);
for (pos=0; /* Nothing */; pos++)
{
if (filenametab != NULL && readmode == Forwardmode)
{
retval = gt_sequence_buffer_next(fb,&ccscan,err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
} else
{
if (pos >= totallength)
{
break;
}
}
ccra = getencodedchar(encseq,pos,readmode); /* Random access */
if (filenametab != NULL && readmode == Forwardmode)
{
if (ccscan != ccra)
{
gt_error_set(err,"access=%s, position=" FormatSeqpos
": scan (readnextchar) = %u != "
"%u = random access",
encseqaccessname(encseq),
pos,
(unsigned int) ccscan,
(unsigned int) ccra);
haserr = true;
break;
}
}
ccsr = sequentialgetencodedchar(encseq,esr,pos,readmode);
if (ccra != ccsr)
{
gt_error_set(err,"access=%s, mode=%s: position=" FormatSeqpos
": random access = %u != %u = sequential read",
encseqaccessname(encseq),
showreadmode(readmode),
pos,
(unsigned int) ccra,
(unsigned int) ccsr);
haserr = true;
break;
}
fullscanpbar++;
}
gt_progressbar_stop();
}
if (!haserr)
{
if (pos != totallength)
{
gt_error_set(err,"sequence length must be " FormatSeqpos " but is "
FormatSeqpos,totallength,pos);
haserr = true;
}
}
freeEncodedsequencescanstate(&esr);
gt_sequence_buffer_delete(fb);
return haserr ? -1 : 0;
}
static void producelongutput(const LTRharvestoptions *lo,
const LTRboundaries *boundaries,
const Encodedsequence *encseq,
Seqpos offset)
{
const GtUchar *characters = getencseqAlphabetcharacters(encseq);
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->leftLTR_5 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->rightLTR_3 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast((boundaries->rightLTR_3 - boundaries->leftLTR_5
+ 1)));
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->leftLTR_5 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->leftLTR_3 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast((boundaries->leftLTR_3 - boundaries->leftLTR_5
+ 1)));
if (lo->minlengthTSD > 1U)
{
Seqpos j;
for (j = 0; j < boundaries->lenleftTSD; j++)
{
printf("%c",(char) characters[getencodedchar(encseq,
boundaries->leftLTR_5 -
boundaries->lenleftTSD + j,
Forwardmode)]);
}
printf(" " FormatSeqpos " ",
PRINTSeqposcast(boundaries->lenleftTSD));
}
if (lo->motif.allowedmismatches < 4U)
{
printf("%c%c..%c%c ",
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_5,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_5+1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_3-1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_3,
Forwardmode)] );
}
/* increase by 1 */
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->rightLTR_5 -offset + 1));
/* increase by 1 */
printf(FormatSeqpos " ",PRINTSeqposcast(boundaries->rightLTR_3 -offset + 1));
printf(FormatSeqpos " ",PRINTSeqposcast(boundaries->rightLTR_3
- boundaries->rightLTR_5 + 1));
if (lo->minlengthTSD > 1U)
{
Seqpos j;
for (j = 0; j < boundaries->lenrightTSD; j++)
{
printf("%c", (char) characters[getencodedchar(encseq,
boundaries->rightLTR_3+j+1,
Forwardmode)]);
}
printf(" " FormatSeqpos " ",PRINTSeqposcast(boundaries->lenrightTSD));
}
if (lo->motif.allowedmismatches < 4U)
{
printf("%c%c..%c%c",
(char) characters[getencodedchar(encseq,/* Randomaccess */
boundaries->rightLTR_5,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Randomaccess */
boundaries->rightLTR_5+1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Randomaccess */
boundaries->rightLTR_3-1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->rightLTR_3,/* Randomaccess */
Forwardmode)] );
}
/* print similarity */
printf(" %.2f", boundaries->similarity);
/* print sequence number */
printf(" %lu\n", boundaries->contignumber);
}