GtRange gth_sa_acceptor_site_range(const GthSA *sa, GtUword intron) { GtRange range; gt_assert(sa); range.end = gth_sa_right_intron_border(sa, intron); range.start = range.end - 1; return range; }
static void xml_showalignmentheader(GthSA *sa, unsigned long minintronlength, unsigned int indentlevel, GtFile *outfp) { unsigned long i, leftreferenceexonborder, rightreferenceexonborder, referenceexonlength; GthDbl exonscore, donorsitescore, acceptorsitescore; GthFlt donorsiteprobability, acceptorsiteprobability; Exoninfo *exoninfo; Introninfo *introninfo; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<predicted_gene_structure>\n"); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<exon-intron_info>\n"); indentlevel++; for (i = 0; i < gth_sa_num_of_exons(sa); i++) { exoninfo = gth_sa_get_exon(sa, i); leftreferenceexonborder = exoninfo->leftreferenceexonborder; rightreferenceexonborder = exoninfo->rightreferenceexonborder; referenceexonlength = rightreferenceexonborder - leftreferenceexonborder + 1; exonscore = exoninfo->exonscore; if (i > 0) { introninfo = gth_sa_get_intron(sa, i-1); donorsiteprobability = introninfo->donorsiteprobability; donorsitescore = introninfo->donorsitescore; acceptorsiteprobability = introninfo->acceptorsiteprobability; acceptorsitescore = introninfo->acceptorsitescore; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<intron i_serial=\"%lu\">\n", i - 1 + OUTPUTOFFSET); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<gDNA_intron_boundary i_start=\"%lu\" i_stop=\"%lu\" " "i_length=\"%lu\">\n", gth_sa_left_intron_border(sa, i-1), gth_sa_right_intron_border(sa, i-1), gth_sa_intron_length(sa, i-1)); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<donor d_prob=\"%.3f\"", donorsiteprobability); if (gth_sa_alphatype(sa) == DNA_ALPHA) gt_file_xprintf(outfp, " d_score=\"%.2f\"", donorsitescore); gt_file_xprintf(outfp, "/>\n"); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<acceptor a_prob=\"%.3f\"", acceptorsiteprobability); if (gth_sa_alphatype(sa) == DNA_ALPHA) gt_file_xprintf(outfp, " a_score=\"%.2f\"", acceptorsitescore); gt_file_xprintf(outfp, "/>\n"); indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</gDNA_intron_boundary>\n"); /* if the intron is shorter or equal than the minimal intron length an additional tag is shown */ if (gth_sa_intron_length(sa, i-1) <= minintronlength) { gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<shorter_than_min_intron_len/>\n"); } indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</intron>\n"); } gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<exon e_serial=\"%lu\">\n", i + OUTPUTOFFSET); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<gDNA_exon_boundary g_start=\"%lu\" g_stop=" "\"%lu\" g_length=\"%lu\"/>\n", gth_sa_left_genomic_exon_border(sa, i), gth_sa_right_genomic_exon_border(sa, i), gth_sa_genomic_exon_length(sa, i)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<reference_exon_boundary r_type=\"%s\" r_start=\"%lu\" " "r_stop=\"%lu\" r_length=\"%lu\" r_score=\"%5.3f\"/>\n", gth_sa_alphastring(sa), leftreferenceexonborder + OUTPUTOFFSET , rightreferenceexonborder + OUTPUTOFFSET , referenceexonlength, exonscore); indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</exon>\n"); } indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</exon-intron_info>\n"); /* showing PPA line (if an poly-A tail was determined) */ if (gth_sa_alphatype(sa) == DNA_ALPHA) xml_showppaline(sa, indentlevel, outfp); /* showing MATCH line */ xml_showmatchline(sa, indentlevel, outfp); /* showing PGS line */ xml_showpgsline(sa, indentlevel, outfp); }
static void showalignmentheader(GthSA *sa, bool gs2out, int widthforgenpos, GtUword minintronlength, GtFile *outfp) { GtUword i, leftreferenceexonborder, rightreferenceexonborder, referenceexonlength; GthDbl exonscore, donorsitescore, acceptorsitescore; GthFlt donorsiteprobability, acceptorsiteprobability; Exoninfo *exoninfo; Introninfo *introninfo; gt_file_xprintf(outfp, "Predicted gene structure"); if (gs2out) { gt_file_xprintf(outfp, " (within gDNA segment "GT_WU" to "GT_WU"):\n", gth_sa_gen_dp_start_show(sa), gth_sa_gen_dp_end_show(sa)); } else gt_file_xprintf(outfp, ":\n"); gt_file_xfputc('\n', outfp); for (i = 0; i < gth_sa_num_of_exons(sa); i++) { exoninfo = gth_sa_get_exon(sa, i); leftreferenceexonborder = exoninfo->leftreferenceexonborder; rightreferenceexonborder = exoninfo->rightreferenceexonborder; referenceexonlength = rightreferenceexonborder - leftreferenceexonborder + 1; exonscore = exoninfo->exonscore; if (i > 0) { introninfo = gth_sa_get_intron(sa, i-1); donorsiteprobability = introninfo->donorsiteprobability; donorsitescore = introninfo->donorsitescore; acceptorsiteprobability = introninfo->acceptorsiteprobability; acceptorsitescore = introninfo->acceptorsitescore; gt_file_xprintf(outfp, " Intron %2" GT_WUS " %*" GT_WUS " %*" GT_WUS " (%4" GT_WUS " n); ", i - 1 + OUTPUTOFFSET, widthforgenpos, gth_sa_left_intron_border(sa, i-1), widthforgenpos, gth_sa_right_intron_border(sa, i-1), gth_sa_intron_length(sa, i-1)); gt_file_xprintf(outfp, "Pd: %5.3f ", donorsiteprobability); if (gth_sa_alphatype(sa) == DNA_ALPHA) { if (donorsitescore == 0.0) gt_file_xprintf(outfp, "(s: 0), "); else gt_file_xprintf(outfp, "(s: %4.2f), ", donorsitescore); } else gt_file_xprintf(outfp, " "); gt_file_xprintf(outfp, "Pa: %5.3f ", acceptorsiteprobability); if (gth_sa_alphatype(sa) == DNA_ALPHA) { if (acceptorsitescore == 0.0) gt_file_xprintf(outfp, "(s: 0)"); else gt_file_xprintf(outfp, "(s: %4.2f)", acceptorsitescore); } /* if the intron is shorter or equal than the minimum intron length two question marks are shown at the end of the line */ if (gth_sa_intron_length(sa, i-1) <= minintronlength) gt_file_xprintf(outfp, " ??"); gt_file_xfputc('\n', outfp); } gt_file_xprintf(outfp, " Exon %2" GT_WUS " %*" GT_WUS " %*" GT_WUS " (%4" GT_WUS " n); %s %6" GT_WUS " %6" GT_WUS " (%4" GT_WUS " %s); " "score: %5.3f\n", i + OUTPUTOFFSET, widthforgenpos, gth_sa_left_genomic_exon_border(sa, i), widthforgenpos, gth_sa_right_genomic_exon_border(sa, i), gth_sa_genomic_exon_length(sa, i), gth_sa_alphastring(sa), leftreferenceexonborder + OUTPUTOFFSET, rightreferenceexonborder + OUTPUTOFFSET, referenceexonlength, gth_sa_alphatype(sa) == DNA_ALPHA ? "n" : "aa", exonscore); } /* showing PPA line (if an poly-A tail was determined) */ if (gth_sa_alphatype(sa) == DNA_ALPHA) showppaline(sa, outfp); gt_file_xfputc('\n', outfp); /* showing MATCH line */ showmatchline(sa, outfp); /* showing PGS line */ showpgsline(sa, outfp); }