/* The following function prints the "classic" GeneSeqer2 MATCH line */ static void xml_showmatchline(GthSA *sa, unsigned int indentlevel, GtFile *outfp) { gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<MATCH_line gen_id=\"%s\" gen_strand=\"%c\" ", gth_sa_gen_id(sa), gth_sa_gen_strand_char(sa)); if (gth_sa_alphatype(sa) == DNA_ALPHA) { gt_file_xprintf(outfp, "ref_id=\"%s\" ref_strand=\"%c\">\n", gth_sa_ref_id(sa), gth_sa_ref_strand_char(sa)); } else gt_file_xprintf(outfp, "ref_id=\"%s\">\n", gth_sa_ref_id(sa)); indentlevel++; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<total_alignment_score>%.3f</total_alignment_score>\n", gth_sa_score(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<cumulative_length_of_scored_exons>%lu" "</cumulative_length_of_scored_exons>\n", gth_sa_cumlen_scored_exons(sa)); gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "<coverage percentage=\"%.3f\" high_type=\"", gth_sa_coverage(sa)); gt_file_xfputc(gth_sa_coverage_char(sa), outfp); gt_file_xprintf(outfp, "\"/>\n"); indentlevel--; gth_indent(outfp, indentlevel); gt_file_xprintf(outfp, "</MATCH_line>\n"); }
/* The following function prints the "classic" GeneSeqer2 MATCH line */ static void showmatchline(GthSA *sa, GtFile *outfp) { gt_file_xprintf(outfp, "MATCH\t%s%c\t%s%c\t%5.3f\t"GT_WU"\t%5.3f\t%c\n", gth_sa_gen_id(sa), gth_sa_gen_strand_char(sa), gth_sa_ref_id(sa), gth_sa_ref_strand_char(sa), gth_sa_score(sa), gth_sa_cumlen_scored_exons(sa), gth_sa_coverage(sa), gth_sa_coverage_char(sa)); }
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"); }