static int storemaxmatchquery(void *info, GT_UNUSED const GtEncseq *encseq, const GtQuerymatch *querymatch, GT_UNUSED const GtUchar *query, GT_UNUSED GtUword query_totallength, GT_UNUSED GtError *err) { GtArray *tab = (GtArray *) info; Substringmatch subm; subm.len = gt_querymatch_querylen(querymatch); subm.dbstart = gt_querymatch_dbstart(querymatch); subm.querystart = gt_querymatch_querystart(querymatch); subm.queryseqnum = gt_querymatch_queryseqnum(querymatch); gt_array_add(tab,subm); return 0; }
static int gt_processxdropquerymatches(void *info, const GtEncseq *encseq, const GtQuerymatch *querymatch, const GtUchar *query, GtUword query_totallength, GtError *err) { GtXdropmatchinfo *xdropmatchinfo = (GtXdropmatchinfo *) info; GtXdropscore score; GtUword querystart, dblen, dbstart, querylen; GtUword pos1 = gt_querymatch_dbstart(querymatch); GtUword pos2 = gt_querymatch_querystart(querymatch); GtUword len = gt_querymatch_querylen(querymatch); const GtUword dbtotallength = gt_encseq_total_length(encseq); uint64_t queryseqnum; GtUword dbseqnum, dbseqstartpos, dbseqlength; dbseqnum = gt_encseq_seqnum(encseq,pos1); dbseqstartpos = gt_encseq_seqstartpos(encseq,dbseqnum); dbseqlength = gt_encseq_seqlength(encseq,dbseqnum); if (pos1 > 0 && pos2 > 0) { gt_assert(dbseqstartpos < pos1); gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,encseq, pos1 - dbseqstartpos,0); gt_seqabstract_reinit_gtuchar(xdropmatchinfo->vseq, query, pos2, 0); gt_evalxdroparbitscoresextend(false, &xdropmatchinfo->best_left, xdropmatchinfo->res, xdropmatchinfo->useq, xdropmatchinfo->vseq, pos1, pos2, xdropmatchinfo->belowscore); } else { xdropmatchinfo->best_left.ivalue = 0; xdropmatchinfo->best_left.jvalue = 0; xdropmatchinfo->best_left.score = 0; } if (pos1 + len < dbtotallength && pos2 + len < query_totallength) { gt_seqabstract_reinit_encseq(xdropmatchinfo->useq, encseq,dbseqstartpos + dbseqlength - (pos1 + len),0); gt_seqabstract_reinit_gtuchar(xdropmatchinfo->vseq, query,query_totallength - (pos2 + len), 0); gt_evalxdroparbitscoresextend(true, &xdropmatchinfo->best_right, xdropmatchinfo->res, xdropmatchinfo->useq, xdropmatchinfo->vseq, pos1 + len, pos2 + len, xdropmatchinfo->belowscore); } else { xdropmatchinfo->best_right.ivalue = 0; xdropmatchinfo->best_right.jvalue = 0; xdropmatchinfo->best_right.score = 0; } gt_assert(pos1 >= (GtUword) xdropmatchinfo->best_left.ivalue && pos2 >= (GtUword) xdropmatchinfo->best_left.jvalue); querystart = pos2 - xdropmatchinfo->best_left.jvalue; queryseqnum = gt_querymatch_queryseqnum(querymatch); dblen = len + xdropmatchinfo->best_left.ivalue + xdropmatchinfo->best_right.ivalue; dbstart = pos1 - xdropmatchinfo->best_left.ivalue; querylen = len + xdropmatchinfo->best_left.jvalue + xdropmatchinfo->best_right.jvalue, score = (GtXdropscore) len * xdropmatchinfo->arbitscores.mat + xdropmatchinfo->best_left.score + xdropmatchinfo->best_right.score; gt_seqabstract_reinit_encseq(xdropmatchinfo->useq, encseq, dblen, dbstart); gt_seqabstract_reinit_gtuchar(xdropmatchinfo->vseq, query, querylen, querystart); gt_querymatch_fill(xdropmatchinfo->querymatchspaceptr, dblen, dbstart, GT_READMODE_FORWARD, false, score, greedyunitedist(xdropmatchinfo->frontresource, xdropmatchinfo->useq,xdropmatchinfo->vseq), false, queryseqnum, querylen, querystart); return gt_querymatch_output(info, encseq, xdropmatchinfo->querymatchspaceptr, query, query_totallength, err); }