/* 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 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);
}
/*
The following function prints the "classic" GeneSeqer2 PGS line
*/
static void showpgsline(GthSA *sa, GtFile *outfp)
{
GtUword i, numofexons;
gt_assert(sa);
numofexons = gth_sa_num_of_exons(sa);
gt_file_xprintf(outfp, "PGS_%s%c_%s%c\t(",
gth_sa_gen_id(sa),
gth_sa_gen_strand_char(sa),
gth_sa_ref_id(sa),
gth_sa_ref_strand_char(sa));
for (i = 0; i < numofexons; i++) {
gt_file_xprintf(outfp, ""GT_WU" "GT_WU"",
gth_sa_left_genomic_exon_border(sa, i),
gth_sa_right_genomic_exon_border(sa, i));
if (i == numofexons - 1)
gt_file_xprintf(outfp, ")\n\n");
else
gt_file_xfputc(',', outfp);
}
}
/*
The following function prints the "classic" GeneSeqer2 PGS line
*/
static void xml_showpgsline(GthSA *sa, unsigned int indentlevel,
GtFile *outfp)
{
unsigned long i, numofexons;
gt_assert(sa);
numofexons = gth_sa_num_of_exons(sa);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<PGS_line>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<gDNA gen_id=\"%s\" gen_strand=\"%c\"/>\n",
gth_sa_gen_id(sa), gth_sa_gen_strand_char(sa));
gth_indent(outfp, indentlevel);
if (gth_sa_alphatype(sa) == DNA_ALPHA) {
gt_file_xprintf(outfp, "<rDNA rDNA_id=\"%s\" rDNA_strand=\"%c\"/>\n",
gth_sa_ref_id(sa), gth_sa_ref_strand_char(sa));
}
else {
gt_file_xprintf(outfp, "<rProt rProt_id=\"%s\"/>\n",
gth_sa_ref_id(sa));
}
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<gDNA_exon_coordinates>\n");
indentlevel++;
for (i = 0; i < numofexons; i++) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon e_start=\"%lu\" e_stop=\"%lu\"/>\n",
gth_sa_left_genomic_exon_border(sa, i),
gth_sa_right_genomic_exon_border(sa, i));
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</gDNA_exon_coordinates>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</PGS_line>\n");
}
