int runsubstringiteration(Greedygmatchforwardfunction gmatchforward,
const void *genericindex,
unsigned long totalwidth,
const unsigned long *leftborder,
const unsigned long *countspecialcodes,
const Alphabet *alphabet,
unsigned int prefixlength,
const GtStrArray *queryfilenames,
GtError *err)
{
GtSeqIterator *seqit;
const GtUchar *query;
unsigned long querylen;
char *desc = NULL;
Substriter *substriter;
Substring substring;
bool haserr = false;
int retval;
unsigned int numofchars;
unsigned long gmatchlength, gmatchlength2;
GtCodetype maxcode;
GtBucketspecification bucketspec;
bool haserr = false;
seqit = gt_seqiterator_new(queryfilenames,getsymbolmapAlphabet(alphabet),
* true);
for (unitnum = 0; ; unitnum++)
{
retval = gt_seqiterator_next(seqit,
&query,
&querylen,
&desc,
err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
}
gt_seqiterator_delete(seqit);
return haserr ? -1 : 0;
}
int runsubstringiteration(Greedygmatchforwardfunction gmatchforward,
const void *genericindex,
unsigned long totalwidth,
const unsigned long *leftborder,
const unsigned long *countspecialcodes,
const Alphabet *alphabet,
unsigned int prefixlength,
const GtStrArray *queryfilenames,
GtError *err)
{
Substriter *substriter;
Substring substring;
bool haserr = false;
int retval;
unsigned int numofchars;
unsigned long gmatchlength, gmatchlength2;
GtCodetype maxcode;
GtBucketspecification bucketspec;
substriter->seqit = gt_seqiterator_new(filenames,
getsymbolmapAlphabet(alphabet),
true);
substriter = gt_substriter_new(queryfilenames,alphabet,prefixlength);
numofchars = getnumofcharsAlphabet(alphabet);
maxcode = ontheflybasepower(numofchars,prefixlength);
while (true)
{
retval = gt_substriter_next(&substring,substriter,err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
gt_assert(substring.remaining >= (unsigned long) prefixlength);
gmatchlength = gmatchforward(genericindex,
0,
0,
totalwidth,
NULL,
substring.currentptr,
substring.currentptr + substring.remaining);
if (leftborder != NULL)
{
gt_bcktab_calcboundaries(&bucketspec,
leftborder,
countspecialcodes,
substring.currentcode,
maxcode,
totalwidth,
substring.currentcode % numofchars,
numofchars);
if (bucketspec.nonspecialsinbucket > 0)
{
gmatchlength2 = gmatchforward(genericindex,
(unsigned long) prefixlength,
bucketspec.left,
bucketspec.left
+ bucketspec.nonspecialsinbucket - 1,
NULL,
substring.currentptr+prefixlength,
substring.currentptr+substring.remaining);
#ifndef NDEBUG
if (gmatchlength2 != gmatchlength)
{
fprintf(stderr,"at offset %lu:\n",(unsigned long)
(substring.currentptr -
substring.start));
fprintf(stderr,"bucketspec=(%lu,%lu)\n",
bucketspec.left,
bucketspec.left+bucketspec.nonspecialsinbucket-1);
fprintf(stderr,"gmatchlength2 = %lu != %lu = gmatchlength\n",
gmatchlength2,gmatchlength);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
#endif
}
}
}
gt_substriter_delete(&substriter);
return haserr ? -1 : 0;
}
int runidxlocali(const IdxlocaliOptions *idxlocalioptions,GtError *err)
{
Genericindex *genericindex = NULL;
bool haserr = false;
Verboseinfo *verboseinfo;
const Encodedsequence *encseq = NULL;
verboseinfo = newverboseinfo(idxlocalioptions->verbose);
if (idxlocalioptions->doonline)
{
encseq = mapencodedsequence (true,
idxlocalioptions->indexname,
true,
false,
false,
true,
verboseinfo,
err);
if (encseq == NULL)
{
haserr = true;
}
} else
{
genericindex = genericindex_new(idxlocalioptions->indexname,
idxlocalioptions->withesa,
idxlocalioptions->withesa ||
idxlocalioptions->docompare,
false,
true,
0,
verboseinfo,
err);
if (genericindex == NULL)
{
haserr = true;
} else
{
encseq = genericindex_getencseq(genericindex);
}
}
if (!haserr)
{
GtSeqIterator *seqit;
const GtUchar *query;
unsigned long querylen;
char *desc = NULL;
int retval;
Limdfsresources *limdfsresources = NULL;
const AbstractDfstransformer *dfst;
SWdpresource *swdpresource = NULL;
Showmatchinfo showmatchinfo;
Processmatch processmatch;
void *processmatchinfoonline, *processmatchinfooffline;
Storematchinfo storeonline, storeoffline;
if (idxlocalioptions->docompare)
{
processmatch = storematch;
initstorematch(&storeonline,encseq);
initstorematch(&storeoffline,encseq);
processmatchinfoonline = &storeonline;
processmatchinfooffline = &storeoffline;
} else
{
processmatch = showmatch;
showmatchinfo.encseq = encseq;
showmatchinfo.characters = getencseqAlphabetcharacters(encseq);
showmatchinfo.wildcardshow = getencseqAlphabetwildcardshow(encseq);
showmatchinfo.showalignment = idxlocalioptions->showalignment;
processmatchinfoonline = processmatchinfooffline = &showmatchinfo;
}
if (idxlocalioptions->doonline || idxlocalioptions->docompare)
{
swdpresource = newSWdpresource(idxlocalioptions->matchscore,
idxlocalioptions->mismatchscore,
idxlocalioptions->gapextend,
idxlocalioptions->threshold,
idxlocalioptions->showalignment,
processmatch,
processmatchinfoonline);
}
dfst = locali_AbstractDfstransformer();
if (!idxlocalioptions->doonline || idxlocalioptions->docompare)
{
gt_assert(genericindex != NULL);
limdfsresources = newLimdfsresources(genericindex,
true,
0,
0, /* maxpathlength */
true, /* keepexpandedonstack */
processmatch,
processmatchinfooffline,
NULL, /* processresult */
NULL, /* processresult info */
dfst);
}
seqit = gt_seqiterator_new(idxlocalioptions->queryfiles, err);
if (!seqit)
haserr = true;
if (!haserr)
{
gt_seqiterator_set_symbolmap(seqit, getencseqAlphabetsymbolmap(encseq));
for (showmatchinfo.queryunit = 0; /* Nothing */;
showmatchinfo.queryunit++)
{
retval = gt_seqiterator_next(seqit,
&query,
&querylen,
&desc,
err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
printf("process sequence " Formatuint64_t " of length %lu\n",
PRINTuint64_tcast(showmatchinfo.queryunit),querylen);
if (idxlocalioptions->doonline || idxlocalioptions->docompare)
{
multiapplysmithwaterman(swdpresource,encseq,query,querylen);
}
if (!idxlocalioptions->doonline || idxlocalioptions->docompare)
{
indexbasedlocali(limdfsresources,
idxlocalioptions->matchscore,
idxlocalioptions->mismatchscore,
idxlocalioptions->gapstart,
idxlocalioptions->gapextend,
idxlocalioptions->threshold,
query,
querylen,
dfst);
}
if (idxlocalioptions->docompare)
{
checkandresetstorematch(showmatchinfo.queryunit,
&storeonline,&storeoffline);
}
gt_free(desc);
}
if (limdfsresources != NULL)
{
freeLimdfsresources(&limdfsresources,dfst);
}
if (swdpresource != NULL)
{
freeSWdpresource(swdpresource);
swdpresource = NULL;
}
gt_seqiterator_delete(seqit);
}
if (idxlocalioptions->docompare)
{
freestorematch(&storeonline);
freestorematch(&storeoffline);
}
}
if (genericindex == NULL)
{
gt_assert(encseq != NULL);
encodedsequence_free((Encodedsequence **) &encseq);
} else
{
genericindex_delete(genericindex);
}
freeverboseinfo(&verboseinfo);
return haserr ? -1 : 0;
}
