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");
}
