static void evalnewexonifpossible(bool proteineop, bool *newexon, bool *newintron, bool *firstexon, bool introncutout, GthSplicedSeq *spliced_seq, Exoninfo *exon, Introninfo *intron, GthSA *sa, Traversealignmentstate *travstate, GtAlphabet *gen_alphabet, GthDPParam *dp_param, GthDPOptionsEST *dp_options_est, const unsigned char *gen_seq_tran, const unsigned char *ref_seq_tran, unsigned long gen_dp_start) { unsigned long splicedpos; if (*newexon) { /* in this case an intron will be saved */ exon->leftgenomicexonborder = gen_dp_start + travstate->genomicptr; exon->leftreferenceexonborder = gt_safe_cast2ulong(travstate->referenceptr); *newexon = false; *newintron = true; if (*firstexon) *firstexon = false; else { /* save acceptorsiteprobability */ if (introncutout) { splicedpos = gth_spliced_seq_orig_to_spliced_pos(spliced_seq, gt_safe_cast2ulong(travstate->genomicptr - 1 + gen_dp_start)); if (splicedpos == GT_UNDEF_ULONG) { /* XXX: no spliced position has been found -> this is an artificially introduced intron, use 0.0 as acceptor site probabilty */ intron->acceptorsiteprobability = 0.0; } else { intron->acceptorsiteprobability = (GthFlt) exp((double) dp_param->log_Pacceptor[splicedpos]); } } else { intron->acceptorsiteprobability = (GthFlt) exp((double) dp_param->log_Pacceptor[travstate->genomicptr-1]); } /* for cDNAs/ESTs: calculationg acceptorsitescore: going forward from here */ if (proteineop) intron->acceptorsitescore = UNDEFINED_SPLICE_SITE_SCORE; else { gthcalcsplicesitescore(&intron->acceptorsitescore, travstate, gen_seq_tran, ref_seq_tran, gen_alphabet, dp_options_est, true); } /* saving the intron */ gth_sa_add_intron(sa, intron); } } }
static void end_element_handler(void *info, const XML_Char *name) { Parseinfo *parseinfo = (Parseinfo*) info; GthSA *sa = parseinfo->currentSA; GtUword datalength; double retdouble; GtWord ret; char *data; /* save data and data length */ data = gt_str_get(parseinfo->databuf); datalength = gt_str_length(parseinfo->databuf); /* perform actions depending on end tag */ if (strcmp(name, SPLICEDALIGNMENT_TAG) == 0) { /* before we store the spliced alignment we have to reverse its edit operations */ gt_assert(sa && gth_sa_backtrace_path(sa)); gth_backtrace_path_reverse(gth_sa_backtrace_path(sa)); /* ensure that before an intron which is not in phase the edit operation has length 1 (only for protein spliced alignments) */ gth_backtrace_path_ensure_length_1_before_introns( gth_sa_backtrace_path(sa)); if (parseinfo->saprocessfunc(parseinfo->data , sa, parseinfo->outputfilename, parseinfo->err)) { /* XXX */ fprintf(stderr, "error: %s\n", gt_error_get(parseinfo->err)); exit(EXIT_FAILURE); } /* reset current spliced alignment */ parseinfo->currentSA = NULL; } else if (strcmp(name, REFERENCEALPHATYPE_TAG) == 0) { if (strcmp(data, "DNA_ALPHA") == 0) gth_sa_set_alphatype(sa, DNA_ALPHA); else if (strcmp(data, "PROTEIN_ALPHA") == 0) { gth_sa_set_alphatype(sa, PROTEIN_ALPHA); } else { ILLEGAL_DATA; } } else if (strcmp(name, DNA_EOP_TYPE_TAG) == 0) { if (strcmp(data, "match") == 0) parseinfo->eoptype = EOP_TYPE_MATCH; else if (strcmp(data, "deletion") == 0) parseinfo->eoptype = EOP_TYPE_DELETION; else if (strcmp(data, "insertion") == 0) parseinfo->eoptype = EOP_TYPE_INSERTION; else if (strcmp(data, "mismatch") == 0) parseinfo->eoptype = EOP_TYPE_MISMATCH; else if (strcmp(data, "intron") == 0) parseinfo->eoptype = EOP_TYPE_INTRON; else { ILLEGAL_DATA; } } else if (strcmp(name, DNA_EOP_LENGTH_TAG) == 0) { SCANUINT; gth_backtrace_path_add_eop(gth_sa_backtrace_path(sa), parseinfo->eoptype, ret); } else if (strcmp(name, PROTEIN_EOP_TYPE_TAG) == 0) { if (strcmp(data, "match") == 0) parseinfo->eoptype = EOP_TYPE_MATCH; else if (strcmp(data, "deletion") == 0) parseinfo->eoptype = EOP_TYPE_DELETION; else if (strcmp(data, "insertion") == 0) parseinfo->eoptype = EOP_TYPE_INSERTION; else if (strcmp(data, "mismatch") == 0) parseinfo->eoptype = EOP_TYPE_MISMATCH; else if (strcmp(data, "intron") == 0) parseinfo->eoptype = EOP_TYPE_INTRON; else if (strcmp(data, "mismatch_with_1_gap") == 0) parseinfo->eoptype = EOP_TYPE_MISMATCH_WITH_1_GAP; else if (strcmp(data, "mismatch_with_2_gaps") == 0) parseinfo->eoptype = EOP_TYPE_MISMATCH_WITH_2_GAPS; else if (strcmp(data, "deletion_with_1_gap") == 0) parseinfo->eoptype = EOP_TYPE_DELETION_WITH_1_GAP; else if (strcmp(data, "deletion_with_2_gaps") == 0) parseinfo->eoptype = EOP_TYPE_DELETION_WITH_2_GAPS; else if (strcmp(data, "intron_with_1_base_left") == 0) parseinfo->eoptype = EOP_TYPE_INTRON_WITH_1_BASE_LEFT; else if (strcmp(data, "intron_with_2_bases_left") == 0) parseinfo->eoptype = EOP_TYPE_INTRON_WITH_2_BASES_LEFT; else { ILLEGAL_DATA; } } else if (strcmp(name, PROTEIN_EOP_LENGTH_TAG) == 0) { SCANUINT; gth_backtrace_path_add_eop(gth_sa_backtrace_path(sa), parseinfo->eoptype, ret); } else if (strcmp(name, INDELCOUNT_TAG) == 0) { SCANUINT; /* ignore indelcount, gets recomputed anyway */ } else if (strcmp(name, GENOMICLENGTHDP_TAG) == 0) { SCANUINT; gth_sa_set_gen_dp_length(sa, ret); } else if (strcmp(name, GENOMICLENGTHTOTAL_TAG) == 0) { SCANUINT; gth_sa_set_gen_total_length(sa, ret); } else if (strcmp(name, GENOMICOFFSET_TAG) == 0) { SCANUINT; gth_sa_set_gen_offset(sa, ret); } else if (strcmp(name, REFERENCELENGTH_TAG) == 0) { SCANUINT; gth_sa_set_ref_total_length(sa, ret); } else if (strcmp(name, DPSTARTPOS_TAG) == 0) { SCANUINT; gth_sa_set_gen_dp_start(sa, ret); } else if (strcmp(name, DPENDPOS_TAG) == 0) { SCANUINT; /* ignore DP end pos, gets recomputed from gen_dp_length anyway */ gt_assert(gth_sa_gen_dp_end(sa) == ret); } else if (strcmp(name, GENOMICFILENAME_TAG) == 0) { /* save genomic file name */ gt_str_append_cstr_nt(parseinfo->genomicfilename, data, datalength); } else if (strcmp(name, GENOMICFILEHASH_TAG) == 0) { gth_sa_set_gen_file_num(sa, process_file(parseinfo->input, gt_str_get(parseinfo->genomicfilename), data, false, UNDEF_ALPHA)); /* reset genomic filename */ gt_str_reset(parseinfo->genomicfilename); } else if (strcmp(name, GENOMICSEQNUM_TAG) == 0) { SCANUINT; gth_sa_set_gen_seq_num(sa, ret); } else if (strcmp(name, REFERENCEFILENAME_TAG) == 0) { /* save reference file name */ gt_str_append_cstr_nt(parseinfo->referencefilename, data, datalength); } else if (strcmp(name, REFERENCEFILEHASH_TAG) == 0) { gth_sa_set_ref_file_num(sa, process_file(parseinfo->input, gt_str_get(parseinfo->referencefilename), data, true, gth_sa_alphatype(sa))); /* reset reference filename */ gt_str_reset(parseinfo->referencefilename); } else if (strcmp(name, REFERENCESEQNUM_TAG) == 0) { SCANUINT; gth_sa_set_ref_seq_num(sa, ret); } else if (strcmp(name, GENOMICID_TAG) == 0) gth_sa_set_gen_id(sa, data); else if (strcmp(name, REFERENCEID_TAG) == 0) gth_sa_set_ref_id(sa, data); else if (strcmp(name, GENOMICSTRANDISFORWARD_TAG) == 0) gth_sa_set_gen_strand(sa, parse_boolean(data, parseinfo)); else if (strcmp(name, REFERENCESTRANDISFORWARD_TAG) == 0) gth_sa_set_ref_strand(sa, parse_boolean(data, parseinfo)); else if (strcmp(name, GENOMICCUTOFF_TAG) == 0) { SCANUINT; parseinfo->cutoffs.genomiccutoff = ret; } else if (strcmp(name, REFERENCECUTOFF_TAG) == 0) { SCANUINT; parseinfo->cutoffs.referencecutoff = ret; } else if (strcmp(name, EOPCUTOFF_TAG) == 0) { SCANUINT; parseinfo->cutoffs.eopcutoff = ret; } else if (strcmp(name, CUTOFFSSTART_TAG) == 0) gth_sa_set_cutoffs_start(sa, &parseinfo->cutoffs); else if (strcmp(name, CUTOFFSEND_TAG) == 0) gth_sa_set_cutoffs_end(sa, &parseinfo->cutoffs); else if (strcmp(name, LEFTGENOMICEXONBORDER_TAG) == 0) { SCANUINT; parseinfo->exoninfo.leftgenomicexonborder = ret; } else if (strcmp(name, RIGHTGENOMICEXONBORDER_TAG) == 0) { SCANUINT; parseinfo->exoninfo.rightgenomicexonborder = ret; } else if (strcmp(name, LEFTREFERENCEEXONBORDER_TAG) == 0) { SCANUINT; parseinfo->exoninfo.leftreferenceexonborder = ret; } else if (strcmp(name, RIGHTREFERENCEEXONBORDER_TAG) == 0) { SCANUINT; parseinfo->exoninfo.rightreferenceexonborder = ret; } else if (strcmp(name, EXONSCORE_TAG) == 0) { SCANDOUBLE; parseinfo->exoninfo.exonscore = retdouble; } else if (strcmp(name, EXONINFO_TAG) == 0) gth_sa_add_exon(sa, &parseinfo->exoninfo); else if (strcmp(name, DONORSITEPROBABILITY_TAG) == 0) { SCANDOUBLE; parseinfo->introninfo.donorsiteprobability = (GthFlt) retdouble; } else if (strcmp(name, ACCEPTORSITEPROBABILITY_TAG) == 0) { SCANDOUBLE; parseinfo->introninfo.acceptorsiteprobability = (GthFlt) retdouble; } else if (strcmp(name, DONORSITESCORE_TAG) == 0) { SCANDOUBLE; parseinfo->introninfo.donorsitescore = retdouble; } else if (strcmp(name, ACCEPTORSITESCORE_TAG) == 0) { SCANDOUBLE; parseinfo->introninfo.acceptorsitescore = retdouble; } else if (strcmp(name, INTRONINFO_TAG) == 0) gth_sa_add_intron(sa, &parseinfo->introninfo); else if (strcmp(name, POLYASTART_TAG) == 0) { SCANUINT; gth_sa_set_polyAtail_start(sa, ret); } else if (strcmp(name, POLYAEND_TAG) == 0) { SCANUINT; gth_sa_set_polyAtail_stop(sa, ret); } else if (strcmp(name, ALIGNMENTSCORE_TAG) == 0) { SCANDOUBLE; gth_sa_set_score(sa, retdouble); } else if (strcmp(name, COVERAGE_TAG) == 0) { SCANDOUBLE; gth_sa_set_coverage(sa, retdouble); } else if (strcmp(name, COVERAGEOFGENOMICSEGMENTISHIGHEST_TAG) == 0) { gth_sa_set_highest_cov(sa, parse_boolean(data, parseinfo)); } else if (strcmp(name, CUMULATIVELENGTHOFSCOREDEXONS_TAG) == 0) { SCANUINT; gth_sa_set_cumlen_scored_exons(sa, ret); } }