static void xml_showgthgenomicinformation(GthSA *sa, GthInput *input, unsigned int indentlevel, GtFile *outfp) { gt_assert(gth_sa_gen_file_num(sa) != GT_UNDEF_ULONG); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<gDNA_segment>\n"); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<template temp_file=\"%s\" temp_id=\"%s\" " "temp_strand=\"%c\" temp_description=\"", gth_input_get_genomic_filename(input, gth_sa_gen_file_num(sa)), gth_sa_gen_id(sa), gth_sa_gen_strand_char(sa)); gth_input_echo_genomic_description(input, gth_sa_gen_file_num(sa), gth_sa_gen_seq_num(sa), outfp); gt_file_xprintf(outfp, "\">\n"); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<position start=\"%lu\" stop=\"%lu\"/>\n", gth_sa_gen_dp_start_show(sa), gth_sa_gen_dp_end_show(sa)); indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</template>\n"); indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</gDNA_segment>\n"); }
static void showgthgenomicinformation(GthSA *sa, GthInput *input, bool showseqnums, GtFile *outfp) { gt_assert(gth_sa_gen_file_num(sa) != GT_UNDEF_UWORD); gt_file_xprintf(outfp, "Genomic Template: file=%s, strand=%c, from="GT_WU", " "to="GT_WU", description=", gth_input_get_genomic_filename(input, gth_sa_gen_file_num(sa)), gth_sa_gen_strand_char(sa), gth_sa_gen_dp_start_show(sa), gth_sa_gen_dp_end_show(sa)); gth_sa_echo_genomic_description(sa, input, outfp); if (showseqnums) gt_file_xprintf(outfp, ", seqnum="GT_WU"", gth_sa_gen_seq_num(sa)); gt_file_xfputc('\n', outfp); gt_file_xfputc('\n', outfp); }
static void xml_inter_show_spliced_alignment(GthSA *sa, GthInput *input, unsigned int indentlevel, GtFile *outfp) { bool dnaalpha = true; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<spliced_alignment xmlns=\"http://www.GenomeThreader.org/" "SplicedAlignment/spliced_alignment/\">\n"); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<referencealphatype>"); switch (gth_sa_alphatype(sa)) { case DNA_ALPHA: gt_file_xprintf(outfp, "DNA_ALPHA"); break; case PROTEIN_ALPHA: gt_file_xprintf(outfp, "PROTEIN_ALPHA"); dnaalpha = false; break; default: gt_assert(0); } gt_file_xprintf(outfp, "</referencealphatype>\n"); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<editoperations>\n"); indentlevel++; gth_backtrace_path_show_complete(gth_sa_backtrace_path(sa), true, indentlevel, outfp); indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</editoperations>\n"); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<indelcount>"GT_WU"</indelcount>\n", gth_sa_indelcount(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<genomiclengthDP>"GT_WU"</genomiclengthDP>\n", gth_sa_gen_dp_length(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<genomiclengthtotal>"GT_WU"</genomiclengthtotal>\n", gth_sa_gen_total_length(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<genomicoffset>"GT_WU"</genomicoffset>\n", gth_sa_gen_offset(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<referencelength>"GT_WU"</referencelength>\n", gth_sa_ref_total_length(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<dpstartpos>"GT_WU"</dpstartpos>\n", gth_sa_gen_dp_start(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<dpendpos>"GT_WU"</dpendpos>\n", gth_sa_gen_dp_end(sa)); showgenomicfilename(sa, input, indentlevel, outfp); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<genomicseqnum>"GT_WU"</genomicseqnum>\n", gth_sa_gen_seq_num(sa)); showreferencefilename(sa, input, indentlevel, outfp); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<referenceseqnum>"GT_WU"</referenceseqnum>\n", gth_sa_ref_seq_num(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<genomicid>%s</genomicid>\n", gth_sa_gen_id(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<referenceid>%s</referenceid>\n", gth_sa_ref_id(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<genomicstrandisforward>%s</genomicstrandisforward>\n", GTH_SHOWBOOL(gth_sa_gen_strand_forward(sa))); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<referencestrandisforward>%s</referencestrandisforward>\n", GTH_SHOWBOOL(gth_sa_ref_strand_forward(sa))); showalignmentcutoffs(sa, indentlevel, outfp); showexons(sa, indentlevel, outfp); showintrons(sa, dnaalpha, indentlevel, outfp); showpolyAtailpos(sa, indentlevel, outfp); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<alignmentscore>%.*f</alignmentscore>\n", PRECISION, gth_sa_score(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<coverage>%.*f</coverage>\n", PRECISION, gth_sa_coverage(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<coverageofgenomicsegmentishighest>%s" "</coverageofgenomicsegmentishighest>\n", GTH_SHOWBOOL(gth_sa_genomic_cov_is_highest(sa))); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<cumulativelengthofscoredexons>"GT_WU"" "</cumulativelengthofscoredexons>\n", gth_sa_cumlen_scored_exons(sa)); indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</spliced_alignment>\n"); }