const void *gt_completealignmentfromLocaliTracebackstate(
GtUword *alignedquerylength,
const Limdfsconstinfo *lci)
{
#ifndef NDEBUG
Scoretype evalscore;
#endif
const GtUchar *querysubstart;
#ifdef SKDEBUG
gt_alignment_show_multieop_list(lci->tbs.alignment,stdout);
#endif
gt_assert(lci->tbs.queryend >= lci->tbs.querypos);
*alignedquerylength = lci->tbs.queryend - lci->tbs.querypos;
querysubstart = lci->query + lci->tbs.querypos;
gt_assert(querysubstart != NULL);
gt_alignment_set_seqs(lci->tbs.alignment,
querysubstart,
*alignedquerylength,
lci->tbs.spaceGtUchardbsubstring,
(GtUword) lci->tbs.dbprefixlen);
#ifndef NDEBUG
evalscore = gt_alignment_eval_with_score(lci->tbs.alignment,false,
lci->scorevalues.matchscore,
lci->scorevalues.mismatchscore,
lci->scorevalues.gapextend);
if (evalscore < 0 || (GtUword) evalscore < lci->threshold)
{
fprintf(stderr,"unexpected eval score "GT_WD"\n",evalscore);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
#endif
return (const void *) lci->tbs.alignment;
}
static void swproducealignment(GtAlignment *alignment,
GtUchar *dbsubstring,
Retracebits *edges,
Scoretype *scol,
const Scorevalues *scorevalues,
GT_UNUSED GtUword scorethreshold,
const GtUchar *useq,
GtUword ulen,
const GtEncseq *vencseq,
GtUword startpos,
GtUword endpos)
{
GtUword vlen = endpos - startpos;
swmaximalDPedges(edges,scol,scorevalues,useq,ulen,vencseq,startpos,endpos);
swtracebackDPedges(alignment,ulen,vencseq,vlen,dbsubstring,startpos,edges);
gt_alignment_set_seqs(alignment,useq,ulen,dbsubstring,(GtUword) vlen);
#ifndef NDEBUG
{
Scoretype evalscore;
evalscore = gt_alignment_eval_with_score(alignment,false,
scorevalues->matchscore,
scorevalues->mismatchscore,
scorevalues->gapextend);
if (evalscore < 0 || (GtUword) evalscore < scorethreshold)
{
fprintf(stderr,"unexpected eval score "GT_WD"\n",evalscore);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
}
#endif
}
GtAlignment* gt_alignment_new_with_seqs(const GtUchar *u, GtUword ulen,
const GtUchar *v, GtUword vlen)
{
GtAlignment *alignment;
gt_assert(u && v);
alignment = gt_alignment_new();
gt_alignment_set_seqs(alignment, u, ulen, v, vlen);
return alignment;
}
/* create an local alignment in square space, to use it in linear context you
* have to generate an spacemanager before, in any other case it can be NULL */
GtWord alignment_in_square_space_local_generic(GtLinspaceManagement
*spacemanager,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen,
const GtScoreHandler
*scorehandler)
{
GtWord score = 0, **Ltabcolumn;
GtMaxcoordvalue *max;
gt_assert(align != NULL);
if (spacemanager == NULL)
{
/*use it in normally case*/
gt_array2dim_malloc(Ltabcolumn, (ulen+1), (vlen+1));
max = gt_max_new();
}
else
{
/*use it in lineraspace context*/
Ltabcolumn = (GtWord **)
gt_linspaceManagement_change_to_square(spacemanager,ulen,vlen);
max = gt_linspaceManagement_get_maxspace(spacemanager);
}
score = fillDPtab_in_square_space_local(Ltabcolumn, max, useq, ustart, ulen,
vseq, vstart, vlen, scorehandler);
/* reconstruct local alignment from 2dimarray Ltabcolumn */
reconstructalignment_from_Ltab(align, Ltabcolumn, max,
useq, ustart, ulen,
vseq,vstart,vlen,scorehandler);
if (gt_max_get_length_safe(max))
{
ustart = ustart+(gt_max_get_start(max)).a;
vstart = vstart+(gt_max_get_start(max)).b;
ulen = gt_max_get_row_length(max);
vlen = gt_max_get_col_length(max);
gt_alignment_set_seqs(align, &useq[ustart], ulen,
&vseq[vstart], vlen);
}
if (spacemanager == NULL)
{
gt_array2dim_delete(Ltabcolumn);
gt_max_delete(max);
}
return score;
}
/* global alignment with linear gapcosts in linear space */
GtUword gt_computelinearspace_generic(LinspaceManagement *spacemanager,
GtScoreHandler *scorehandler,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen)
{
GtUword distance;
gt_assert(spacemanager && scorehandler && align);
gt_alignment_set_seqs(align, useq+ustart, ulen, vseq+vstart, vlen);
distance = gt_calc_linearalign(spacemanager, scorehandler, align,
useq, ustart, ulen,
vseq, vstart, vlen);
return distance;
}
/* determining start and end of local alignment and call global function */
GtWord gt_computelinearspace_local_generic(LinspaceManagement *spacemanager,
GtScoreHandler *scorehandler,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen)
{
GtWord *Ltabcolumn, GT_UNUSED score = GT_WORD_MAX;
GtUwordPair *Starttabcolumn;
GtUword ulen_part, ustart_part, vlen_part, vstart_part;
Gtmaxcoordvalue *max;
gt_assert(spacemanager && scorehandler && align);
gt_linspaceManagement_set_ulen(spacemanager,ulen);
if (ulen == 0UL || vlen == 0UL)
{
/* empty alignment */
return 0;
}
else if (vlen == 1UL)
{
gt_linspaceManagement_check_local(spacemanager,
(ulen+1)*(vlen+1)-1, ulen,
sizeof (GtWord),
sizeof (GtWord *));
return alignment_in_square_space_local_generic(spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen,
scorehandler);
}
else if (gt_linspaceManagement_checksquare_local(spacemanager, ulen, vlen,
sizeof (*Ltabcolumn),
sizeof (*Starttabcolumn)))
{
/* call 2dim */
return alignment_in_square_space_local_generic(spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen,
scorehandler);
}
gt_linspaceManagement_check_local(spacemanager,
ulen, vlen,
sizeof (*Ltabcolumn),
sizeof (*Starttabcolumn));
max = evaluateallLScolumns(spacemanager, scorehandler,
useq, ustart, ulen,
vseq, vstart, vlen);
if (gt_max_get_length_safe(max))
{
ustart_part = ustart+(gt_max_get_start(max)).a;
vstart_part = vstart+(gt_max_get_start(max)).b;
ulen_part = gt_max_get_row_length(max);
vlen_part = gt_max_get_col_length(max);
score = gt_max_get_value(max);
gt_scorehandler_change_score_to_cost(scorehandler);
gt_alignment_set_seqs(align, &useq[ustart_part], ulen_part,
&vseq[vstart_part], vlen_part);
/* call global function */
gt_calc_linearalign(spacemanager,
gt_scorehandler_get_costhandler(scorehandler), align,
useq, ustart_part, ulen_part,
vseq, vstart_part, vlen_part);
} else
{
/*empty alignment */
return 0;
}
return score;
}