static void show_spliced_alignment(GthSA *sa, GthInput *input, bool gs2out,
GtUword minintronlength,
GtUword widthforgenpos,
GtUword showintronmaxlen,
GtUword translationtable,
bool showseqnums, GtFile *outfp)
{
bool wildcardimplosion = false;
showdelimiterline(outfp);
if (gs2out) {
/* all wildcards (N,S,Y,W,R,K,V,B,D,H,M) will be replaced by the wildcard N
makes only sense for a DNA alphabet */
wildcardimplosion = true;
showgs2referenceinformation(sa, outfp);
gth_sa_echo_reference_sequence(sa, input, true, outfp);
}
else {
showgthreferenceinformation(sa, input, showseqnums, outfp);
gth_sa_echo_reference_sequence(sa, input, true, outfp);
showgthgenomicinformation(sa, input, showseqnums, outfp);
}
showalignmentheader(sa, gs2out, widthforgenpos, minintronlength, outfp);
gt_file_xprintf(outfp,
"Alignment (genomic DNA sequence = upper lines):\n\n");
gth_sa_echo_alignment(sa, showintronmaxlen, translationtable,
wildcardimplosion, input, outfp);
}
static void xml_final_show_spliced_alignment(GthSA *sa, GthInput *input,
unsigned long minintronlength,
unsigned long translationtable,
unsigned int indentlevel,
GtFile *outfp)
{
unsigned char *first_line, *second_line, *third_line;
GT_UNUSED bool reverse_subject_pos = false;
unsigned long cols;
gt_assert(sa && input);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<spliced_alignment xmlns=\"http://www.genomethreader.org/"
"GTH_output/alignment_module/spliced_alignment/\">\n");
indentlevel++;
/* If the reverse complement of the genomic DNA is considered, this
opition is needed for correct output of the genomic sequence positions
by the function showalignmentgeneric() */
if (!gth_sa_gen_strand_forward(sa))
reverse_subject_pos = true;
xml_showgthreferenceinformation(sa, input, indentlevel, outfp);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<seq>");
gth_sa_echo_reference_sequence(sa, input, false, outfp);
gt_file_xprintf(outfp, "</seq>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</reference>\n");
xml_showgthgenomicinformation(sa, input, indentlevel, outfp);
xml_showalignmentheader(sa, minintronlength, indentlevel, outfp);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<alignment>\n");
/* compute the alignment lines */
cols = gth_sa_get_alignment_lines(sa, &first_line, &second_line, &third_line,
translationtable, input);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genome_strand>");
showconcreteline(first_line, cols, outfp);
gt_file_xprintf(outfp, "</genome_strand>\n");
gth_indent(outfp, indentlevel);
switch (gth_sa_alphatype(sa)) {
case DNA_ALPHA:
gt_file_xprintf(outfp, "<mrna_strand>");
showconcreteline(second_line, cols, outfp);
gt_file_xprintf(outfp, "</mrna_strand>\n");
break;
case PROTEIN_ALPHA:
gt_file_xprintf(outfp, "<genomeProt>");
showconcreteline(second_line, cols, outfp);
gt_file_xprintf(outfp, "</genomeProt>\n");
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<queryProt>");
showconcreteline(third_line, cols, outfp);
gt_file_xprintf(outfp, "</queryProt>\n");
break;
default: gt_assert(0);
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</alignment>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</predicted_gene_structure>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</spliced_alignment>\n");
/* free */
gt_free(first_line);
gt_free(second_line);
gt_free(third_line);
}
