/* test the motif and encode the characters by using alpha */
int testmotifandencodemotif (Motif *motif, const Encodedsequence *encseq,
GtError *err)
{
const GtUchar *symbolmap;
GtUchar c_tab[UCHAR_MAX+1];
unsigned int i;
symbolmap = getencseqAlphabetsymbolmap(encseq);
if ( symbolmap[(unsigned int)motif->firstleft] == (GtUchar) UNDEFCHAR)
{
gt_error_set(err,"Illegal nucleotide character %c "
"as argument to option -motif", motif->firstleft);
return -1;
}
if ( symbolmap[(unsigned int)motif->secondleft] == (GtUchar) UNDEFCHAR )
{
gt_error_set(err,"Illegal nucleotide character %c "
"as argument to option -motif", motif->secondleft);
return -1;
}
if ( symbolmap[(unsigned int)motif->firstright] == (GtUchar) UNDEFCHAR )
{
gt_error_set(err,"Illegal nucleotide character %c "
"as argument to option -motif", motif->firstright);
return -1;
}
if ( symbolmap[(unsigned int)motif->secondright] == (GtUchar) UNDEFCHAR )
{
gt_error_set(err,"Illegal nucleotide character %c "
"as argument to option -motif", motif->secondright);
return -1;
}
for (i=0; i<=(unsigned int) UCHAR_MAX; i++)
{
c_tab[i] = (GtUchar) UNDEFCHAR;
}
/* define complementary symbols */
c_tab[symbolmap['a']] = symbolmap['t'];
c_tab[symbolmap['c']] = symbolmap['g'];
c_tab[symbolmap['g']] = symbolmap['c'];
c_tab[symbolmap['t']] = symbolmap['a'];
/* if motif is not palindromic */
if ( (c_tab[symbolmap[(unsigned int)motif->firstleft]] !=
c_tab[c_tab[symbolmap[(unsigned int)motif->secondright]]])
||
(c_tab[symbolmap[(unsigned int)motif->secondleft]] !=
c_tab[c_tab[symbolmap[(unsigned int)motif->firstright]]]) )
{
gt_error_set(err, "Illegal motif, motif not palindromic");
return -1;
}
/* encode the symbols */
motif->firstleft = symbolmap[(unsigned int)motif->firstleft];
motif->secondleft = symbolmap[(unsigned int)motif->secondleft];
motif->firstright = symbolmap[(unsigned int)motif->firstright];
motif->secondright = symbolmap[(unsigned int)motif->secondright];
return 0;
}
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;
}
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;
}
