GtTranslator* gt_translator_new(GtCodonIterator *ci)
{
GtTranslator *tr;
gt_assert(ci);
tr = gt_translator_new_with_table(gt_trans_table_new_standard(NULL), ci);
tr->owntable = true;
return tr;
}
void gt_outputtranslationandorf(unsigned long pglnum, const GthAGS *ags,
unsigned long agsnum,
unsigned long translationtable,
GthInput *input,
unsigned int indentlevel,
GthOutput *out)
{
unsigned long i;
unsigned int nframe;
const unsigned char *gen_seq_orig;
GtStr *frame[3];
char translated;
GtTranslatorStatus status;
GtTranslator *translator;
GtTransTable *transtable;
GtCodonIterator *ci;
GthSplicedSeq *spliced_seq;
GtArray *ranges;
GtFile *outfp = out->outfp;
/* output header */
if (out->xmlout) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<three_phase_translation "
"xmlns=\"http://www.genomethreader.org/GTH_output/"
"PGL_module/predicted_gene_location/AGS_information/"
"three_phase_translation/\">\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<description PGL_serial=\"%lu\" "
"AGS_serial=\"%lu\" gDNA_strand=\"%c\"/>\n",
pglnum + OUTPUTOFFSET, agsnum + OUTPUTOFFSET,
SHOWSTRAND(gth_ags_is_forward(ags)));
}
else {
gt_file_xprintf(outfp, "3-phase translation of AGS-%lu (%cstrand):\n\n",
agsnum + OUTPUTOFFSET,
SHOWSTRAND(gth_ags_is_forward(ags)));
}
ranges = gt_array_new(sizeof (GtRange));
for (i = 0; i < gt_array_size(ags->exons); i++)
gt_array_add(ranges, ((GthExonAGS*) gt_array_get(ags->exons, i))->range);
/* get genomic sequence */
gen_seq_orig = gth_input_original_genomic_sequence(input,
gth_ags_filenum(ags),
gth_ags_is_forward(ags));
spliced_seq = gth_spliced_seq_new(gen_seq_orig, ranges);
frame[0] = gt_str_new();
frame[1] = gt_str_new();
frame[2] = gt_str_new();
/* prepare for translation */
ci = gt_codon_iterator_simple_new((const char*) spliced_seq->splicedseq,
spliced_seq->splicedseqlen, NULL);
gt_assert(ci);
transtable = gt_trans_table_new(translationtable, NULL);
gt_assert(transtable);
/* translate the template in all three frames */
translator = gt_translator_new_with_table(transtable, ci);
status = gt_translator_next(translator, &translated, &nframe, NULL);
while (status == GT_TRANSLATOR_OK) {
gt_str_append_char(frame[nframe], translated);
status = gt_translator_next(translator, &translated, &nframe, NULL);
}
gt_assert(status != GT_TRANSLATOR_ERROR);
gt_translator_delete(translator);
gt_trans_table_delete(transtable);
gt_codon_iterator_delete(ci);
/* show the translation */
showtranslation(spliced_seq, gt_str_get(frame[0]), gt_str_get(frame[1]),
gt_str_get(frame[2]), ags->exons, gth_ags_is_forward(ags),
gth_ags_total_length(ags), gth_ags_genomic_offset(ags),
indentlevel, out);
/* show the (consolidated) ORFs */
gthshowORFs(gt_str_get(frame[0]), gt_str_get(frame[1]), gt_str_get(frame[2]),
gt_str_length(frame[0]), gt_str_length(frame[1]),
gt_str_length(frame[2]), gth_ags_is_forward(ags),
gth_ags_total_length(ags), gth_ags_genomic_offset(ags),
gt_str_get(ags->gen_id), pglnum, agsnum, spliced_seq,
indentlevel, out);
if (out->xmlout) {
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</three_phase_translation>\n");
}
gth_spliced_seq_delete(spliced_seq);
gt_array_delete(ranges);
gt_str_delete(frame[0]);
gt_str_delete(frame[1]);
gt_str_delete(frame[2]);
}
