static void xml_show_pgl(GthPGL *pgl, unsigned long pglnum,
unsigned long translationtable, GthInput *input,
unsigned int indentlevel, GthOutput *out)
{
unsigned long i;
gth_indent(out->outfp, indentlevel);
gt_file_xprintf(out->outfp, "<predicted_gene_location>\n");
indentlevel++;
gth_indent(out->outfp, indentlevel);
gt_file_xprintf(out->outfp,
"<PGL_line PGL_serial=\"%lu\" PGL_strand=\"%c\" "
"PGL_start=\"%lu\" PGL_stop=\"%lu\"/>\n",
pglnum + OUTPUTOFFSET,
SHOWSTRAND(gth_pgl_is_forward(pgl)),
SHOWGENPOS(gth_pgl_is_forward(pgl),
gth_pgl_total_length(pgl),
gth_pgl_genomic_offset(pgl),
pgl->maxrange.start),
SHOWGENPOS(gth_pgl_is_forward(pgl),
gth_pgl_total_length(pgl),
gth_pgl_genomic_offset(pgl),
pgl->maxrange.end));
for (i = 0; i < gth_pgl_num_of_ags(pgl); i++) {
xml_show_ags(gth_pgl_get_ags(pgl, i), pglnum, i, translationtable, input,
indentlevel, out);
}
indentlevel--;
gth_indent(out->outfp, indentlevel);
gt_file_xprintf(out->outfp, "</predicted_gene_location>\n");
}
static void show_pgl(GthPGL *pgl, GtUword pglnum,
GtUword translationtable, GthInput *input,
unsigned int indentlevel, GthOutput *out)
{
GtUword i;
GtFile *outfp = out->outfp;
gt_assert(!out->gff3out);
if (out->xmlout) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<predicted_gene_location>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<PGL_line PGL_serial=\"" GT_WU "\" "
"PGL_strand=\"%c\" PGL_start=\"" GT_WU "\" PGL_stop=\""
GT_WU "\"/>\n",
pglnum + OUTPUTOFFSET,
SHOWSTRAND(gth_pgl_is_forward(pgl)),
SHOWGENPOS(gth_pgl_is_forward(pgl),
gth_pgl_total_length(pgl),
gth_pgl_genomic_offset(pgl),
pgl->maxrange.start),
SHOWGENPOS(gth_pgl_is_forward(pgl),
gth_pgl_total_length(pgl),
gth_pgl_genomic_offset(pgl),
pgl->maxrange.end));
}
else {
gt_file_xprintf(outfp, "PGL %3" GT_WUS " (%c strand): " GT_WU " "
GT_WU,
pglnum + OUTPUTOFFSET,
SHOWSTRAND(gth_pgl_is_forward(pgl)),
SHOWGENPOS(gth_pgl_is_forward(pgl),
gth_pgl_total_length(pgl),
gth_pgl_genomic_offset(pgl),
pgl->maxrange.start),
SHOWGENPOS(gth_pgl_is_forward(pgl),
gth_pgl_total_length(pgl),
gth_pgl_genomic_offset(pgl),
pgl->maxrange.end));
if (out->pglgentemplate)
gt_file_xprintf(outfp, " (genomic template '%s')", gth_pgl_gen_id(pgl));
gt_file_xfputc('\n', outfp);
}
for (i = 0; i < gt_array_size(pgl->assemblies); i++) {
show_ags(gth_pgl_get_ags(pgl, i), pglnum, i, translationtable, input,
indentlevel, out);
}
if (out->xmlout) {
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</predicted_gene_location>\n");
}
}
GtUword gth_sa_gen_dp_end_show(const GthSA *sa)
{
gt_assert(sa);
return SHOWGENPOS(sa->gen_strand_forward,
sa->gen_total_length,
sa->gen_offset,
gth_sa_gen_dp_start(sa) + gth_sa_gen_dp_length(sa) - 1);
}
GtUword gth_sa_gen_dp_start_show(const GthSA *sa)
{
gt_assert(sa);
return SHOWGENPOS(sa->gen_strand_forward,
sa->gen_total_length,
sa->gen_offset,
gth_backtrace_path_gen_dp_start(sa->backtrace_path));
}
GtUword gth_sa_right_intron_border(const GthSA *sa, GtUword intron)
{
Exoninfo *exoninfo;
gt_assert(sa);
exoninfo = gth_sa_get_exon(sa, intron + 1);
return SHOWGENPOS(sa->gen_strand_forward,
sa->gen_total_length,
sa->gen_offset,
exoninfo->leftgenomicexonborder - 1);
}
static void showoutputlines(char *dotline,
char *template_out,
char *frame0_out,
char *frame1_out,
char *frame2_out,
unsigned long outlen,
bool gen_strand_forward,
unsigned long gen_total_length,
unsigned long gen_offset,
unsigned long *positionmapping,
GthOutput *out)
{
unsigned long i, outcounter = 0, origcounter = 0;
while (outcounter < outlen) {
OUTPUT_EXONPOSSPACE;
OUTPUT_LINE(dotline);
/* output exon position */
gt_file_xprintf(out->outfp, "%*lu ", out->widthforgenpos,
SHOWGENPOS(gen_strand_forward, gen_total_length,
gen_offset, positionmapping[origcounter]));
OUTPUT_LINE(template_out);
OUTPUT_EXONPOSSPACE;
OUTPUT_LINE(frame0_out);
OUTPUT_EXONPOSSPACE;
OUTPUT_LINE(frame1_out);
OUTPUT_EXONPOSSPACE;
OUTPUT_LINE(frame2_out);
(void) gt_file_xprintf(out->outfp, "\n\n");
outcounter = i + 1;
origcounter += TRANSLATIONLINEWIDTH;
}
}