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 xml_outputAGSline(const GthAGS *ags, unsigned long agsnum,
unsigned int indentlevel, GtFile *outfp)
{
GthExonAGS *exon;
unsigned long i;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<AGS_line AGS_serial=\"%lu\">\n",
agsnum + OUTPUTOFFSET);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon_coordinates>\n");
indentlevel++;
for (i = 0; i < gth_ags_num_of_exons(ags); i++) {
exon = gth_ags_get_exon(ags, i);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon e_start=\"%lu\" e_stop=\"%lu\"/>\n",
SHOWGENPOSAGS(exon->range.start),
SHOWGENPOSAGS(exon->range.end));
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon_coordinates>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</AGS_line>\n");
}
static void xml_outputSCRline(const GthAGS *ags, unsigned int indentlevel,
GtFile *outfp)
{
GthSpliceSiteProb *splicesiteprob;
unsigned long i;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<SCR_line>\n");
indentlevel++;
for (i = 0; i < gt_array_size(ags->exons) - 1; i++) {
splicesiteprob = (GthSpliceSiteProb*) gt_array_get(ags->splicesiteprobs, i);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon-intron don_prob=\"%.3f\" "
"acc_prob=\"%.3f\" e_score=\"%.3f\"/>\n",
splicesiteprob->donorsiteprob,
splicesiteprob->acceptorsiteprob,
((GthExonAGS*) gt_array_get(ags->exons, i))->score);
}
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon-only e_score=\"%.3f\"/>\n",
((GthExonAGS*) gt_array_get(ags->exons, i))->score);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</SCR_line>\n");
}
static void xml_show_ags(const GthAGS *ags, unsigned long pglnum,
unsigned long agsnum, unsigned long translationtable,
GthInput *input, unsigned int indentlevel,
GthOutput *out)
{
gth_indent(out->outfp, indentlevel);
gt_file_xprintf(out->outfp, "<AGS_information>\n");
indentlevel++;
/* output AGS line */
xml_outputAGSline(ags, agsnum, indentlevel, out->outfp);
/* output SCR line */
xml_outputSCRline(ags, indentlevel, out->outfp);
/* output exon/intron lines */
xml_output_exon_intron_lines(ags, indentlevel, out->outfp);
/* output PGS lines */
xml_outputPGSlines(ags->alignments, indentlevel, out->outfp);
/* output 3-phase translation */
gt_outputtranslationandorf(pglnum, ags, agsnum, translationtable, input,
indentlevel, out);
indentlevel--;
gth_indent(out->outfp, indentlevel);
gt_file_xprintf(out->outfp, "</AGS_information>\n");
}
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");
}
/* 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");
}
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");
}
}
static void xml_final_sa_visitor_trailer(GthSAVisitor *sa_visitor,
unsigned long num_of_sas)
{
GthXMLFinalSAVisitor *visitor = xml_final_sa_visitor_cast(sa_visitor);
visitor->indentlevel++;
gth_indent(visitor->outfp, visitor->indentlevel);
gt_file_xprintf(visitor->outfp, "<total_number_ESTs_reported>%lu"
"</total_number_ESTs_reported>\n", num_of_sas);
gth_indent(visitor->outfp, visitor->indentlevel);
gt_file_xprintf(visitor->outfp, "</alignment_module>\n");
visitor->indentlevel--;
}
static void xml_showgthreferenceinformation(GthSA *sa,
GthInput *input,
unsigned int indentlevel,
GtFile *outfp)
{
gt_assert(gth_sa_ref_file_num(sa) != GT_UNDEF_ULONG);
gth_indent(outfp, indentlevel);
switch (gth_sa_alphatype(sa)) {
case DNA_ALPHA:
gt_file_xprintf(outfp, "<reference ref_file=\"%s\" ref_id=\"%s\" "
"ref_strand=\"%c\" ref_description=\"",
gth_input_get_reference_filename(input,
gth_sa_ref_file_num(sa)),
gth_sa_ref_id(sa),
gth_sa_ref_strand_char(sa));
break;
case PROTEIN_ALPHA:
gt_file_xprintf(outfp, "<reference ref_file=\"%s\" ref_id=\"%s\" "
"ref_description=\"",
gth_input_get_reference_filename(input,
gth_sa_ref_file_num(sa)),
gth_sa_ref_id(sa));
break;
default: gt_assert(0);
}
gth_input_echo_reference_description(input, gth_sa_ref_file_num(sa),
gth_sa_ref_seq_num(sa), outfp);
gt_file_xprintf(outfp, "\">\n");
}
static void xml_pgl_visitor_preface(GthPGLVisitor *pgl_visitor,
GT_UNUSED unsigned long num_of_pgls)
{
GthXMLPGLVisitor *visitor = xml_pgl_visitor_cast(pgl_visitor);
gth_indent(visitor->out->outfp, visitor->indentlevel);
gt_file_xprintf(visitor->out->outfp,
"<PGL_module xmlns=\"http://www.genomethreader."
"org/GTH_output/PGL_module/\">\n");
}
static void showpolyAtailpos(GthSA *sa, unsigned int indentlevel,
GtFile *outfp)
{
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<polyAtailpos>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<polyAstart>"GT_WU"</polyAstart>\n",
gth_sa_polyAtail_start(sa));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<polyAstop>"GT_WU"</polyAstop>\n",
gth_sa_polyAtail_stop(sa));
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</polyAtailpos>\n");
}
static void showgenomicfilename(GthSA *sa, GthInput *input,
unsigned int indentlevel, GtFile *outfp)
{
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomicfile>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomicfilename>%s</genomicfilename>\n",
gth_input_get_genomic_filename(input,
gth_sa_gen_file_num(sa)));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomicfilehash>%s</genomicfilehash>\n",
GTH_UNDEFINED_HASH);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</genomicfile>\n");
}
static void xml_outputPGSlines(GtArray *alignments, unsigned int indentlevel,
GtFile *outfp)
{
unsigned long i, j;
GthSA *sa;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<supporting_evidence xmlns=\""
"http://www.genomethreader.org/"
"GTH_output/PGL_module/predicted_gene_location/"
"AGS_information/supporting_evidence/\">\n");
indentlevel++;
for (i = 0; i < gt_array_size(alignments); i++) {
sa = *(GthSA**) gt_array_get(alignments, i);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<PGS_line>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<gDNA_exon_coordinates>\n");
indentlevel++;
for (j = 0; j < gth_sa_num_of_exons(sa); j++) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon start=\"%lu\" stop=\"%lu\"/>\n",
gth_sa_left_genomic_exon_border(sa, j),
gth_sa_right_genomic_exon_border(sa, j));
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</gDNA_exon_coordinates>\n");
gth_indent(outfp, indentlevel);
if (gth_sa_alphatype(sa) == DNA_ALPHA) {
gt_file_xprintf(outfp, "<referenceDNA id=\"%s\" strand=\"%c\"/>\n",
gth_sa_ref_id(sa),
gth_sa_ref_strand_char(sa));
}
else {
gt_file_xprintf(outfp, "<referenceProtein id=\"%s\"/>\n",
gth_sa_ref_id(sa));
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</PGS_line>\n");
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</supporting_evidence>\n");
}
/*
The following function prints a PPA line, which shows the start and end
position of the poly-A tail in the cDNA (iff a poly-A tail could be
determined).
*/
static void xml_showppaline(GthSA *sa, unsigned int indentlevel,
GtFile *outfp)
{
if (gth_sa_polyAtail_start(sa) ||
gth_sa_polyAtail_stop(sa)) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<PPA_line polyA_start=\"%lu\" polyA_stop=\"%lu\"/>\n",
gth_sa_polyAtail_start(sa) + OUTPUTOFFSET,
gth_sa_polyAtail_stop(sa) + OUTPUTOFFSET);
}
}
static void show_overall_reference_type(GthAlphatype overallalphatype,
unsigned int indentlevel,
GtFile *outfp)
{
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<overall_reference_type>");
switch (overallalphatype)
{
case DNA_ALPHA:
gt_file_xprintf(outfp, "ESTcDNA");
break;
case PROTEIN_ALPHA:
gt_file_xprintf(outfp, "Protein");
break;
case MIXED_ALPHA:
gt_file_xprintf(outfp, "Mixed");
break;
default: gt_assert(0);
}
gt_file_xprintf(outfp, "</overall_reference_type>\n");
}
/*
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");
}
static void showexons(GthSA *sa, unsigned int indentlevel,
GtFile *outfp)
{
Exoninfo *exoninfo;
GtUword i;
for (i = 0; i < gth_sa_num_of_exons(sa); i++) {
exoninfo = gth_sa_get_exon(sa, i);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exoninfo>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<leftgenomicexonborder>"GT_WU"</leftgenomicexonborder>\n",
exoninfo->leftgenomicexonborder);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<rightgenomicexonborder>"GT_WU
"</rightgenomicexonborder>\n",
exoninfo->rightgenomicexonborder);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<leftreferenceexonborder>"GT_WU
"</leftreferenceexonborder>\n",
exoninfo->leftreferenceexonborder);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<rightreferenceexonborder>"GT_WU
"</rightreferenceexonborder>\n",
exoninfo->rightreferenceexonborder);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exonscore>%.*f</exonscore>\n", PRECISION,
exoninfo->exonscore);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exoninfo>\n");
}
}
static void showintrons(GthSA *sa, bool dnaalpha,
unsigned int indentlevel, GtFile *outfp)
{
Introninfo *introninfo;
GtUword i;
for (i = 0; i < gth_sa_num_of_introns(sa); i++) {
introninfo = gth_sa_get_intron(sa, i);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<introninfo>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<donorsiteprobability>%.*f</donorsiteprobability>\n",
PRECISION, introninfo->donorsiteprobability);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<acceptorsiteprobability>%.*f</acceptorsiteprobability>\n",
PRECISION, introninfo->acceptorsiteprobability);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<donorsitescore>%.*f</donorsitescore>\n",
PRECISION,
dnaalpha ? introninfo->donorsitescore
: UNDEFINED_SPLICE_SITE_SCORE);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<acceptorsitescore>%.*f</acceptorsitescore>\n",
PRECISION,
dnaalpha ? introninfo->acceptorsitescore
: UNDEFINED_SPLICE_SITE_SCORE);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</introninfo>\n");
}
}
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");
}
static void show_xml_run_header(GthCallInfo *call_info, GthInput *input,
const char *timestring, const char *gth_version,
unsigned int indentlevel, const char **args)
{
GtFile *outfp = call_info->out->outfp;
GtUword i;
gth_indent(outfp, indentlevel);
if (call_info->intermediate) {
gt_file_xprintf(outfp, "<header xmlns=\"http://www.GenomeThreader.org/"
"SplicedAlignment/header/\">\n");
}
else {
gt_file_xprintf(outfp,
"<header xmlns=\"http://www.genomethreader.org/GTH_output/"
"header/\">\n");
}
/* at least one genomic file defined */
gt_assert(gth_input_num_of_gen_files(input));
/* at least one reference file defined */
gt_assert(gth_input_num_of_ref_files(input));
/* show a readable version of GthCallInfo. That is, it is shown with wich
parameters the program was called */
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<source program=\"GenomeThreader\" version=\"%s\" "
"build_date=\"%s\" run_date=\"%s\"/>\n", gth_version,
GT_BUILT, timestring);
/* show genomic file names */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<gDNA_template_files>\n");
indentlevel++;
for (i = 0; i < gth_input_num_of_gen_files(input); i++) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<temp_name>%s</temp_name>\n",
gth_input_get_genomic_filename(input, i));
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</gDNA_template_files>\n");
/* show reference file names */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<reference_files>\n");
indentlevel++;
for (i = 0; i < gth_input_num_of_ref_files(input); i++) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<file ref_name=\"%s\" type=\"%s\"/>\n",
gth_input_get_reference_filename(input, i),
gth_input_get_alphatype(input, i) == DNA_ALPHA
? "ESTcDNA" : "Protein");
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</reference_files>\n");
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<splice_site_parameters parameter_type=\"%s\" "
"species=\"%s\"/>\n", SPLICE_SITE_MODEL_NAME,
call_info->speciesnum == NUMOFSPECIES
? GENERIC_SPECIES_NAME
: speciestab[call_info->speciesnum]);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<parameters>\n");
indentlevel++;
/* output name of BSSM file */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<parameter name=\"bssmfile\" value=\"%s\"/>\n",
gth_input_bssmfilename(input));
/* output name of scorematrix */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<parameter name=\"scorematrixfile\" value=\"%s\"/>\n",
gt_str_get(call_info->scorematrixfile));
/* output searchmode */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<parameter name=\"searchmode\" "
"value=\"forward=%s,reverse=%s)\"/>\n",
GTH_SHOWBOOL(gth_input_forward(input)),
GTH_SHOWBOOL(gth_input_reverse(input)));
/* output arguments as comment */
gt_file_xprintf(outfp, "<!--\n%c Arguments: ", COMMENTCHAR);
gt_cstr_array_show_genfile(args, outfp);
gt_file_xprintf(outfp, "-->\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</parameters>\n");
show_overall_reference_type(gth_input_overall_alphatype(input),
indentlevel, outfp);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</header>\n");
}
static void xml_pgl_visitor_trailer(GthPGLVisitor *pgl_visitor)
{
GthXMLPGLVisitor *visitor = xml_pgl_visitor_cast(pgl_visitor);
gth_indent(visitor->out->outfp, visitor->indentlevel);
gt_file_xprintf(visitor->out->outfp, "</PGL_module>\n");
}
static void xml_output_exon_intron_lines(const GthAGS *ags,
unsigned int indentlevel,
GtFile *outfp)
{
GthSpliceSiteProb *splicesiteprob;
GthExonAGS *exon;
unsigned long i, leftexonborder, rightexonborder, exonlength,
leftintronborder = GT_UNDEF_ULONG, rightintronborder,
intronlength;
GthDbl exonscore;
GthFlt donorsiteprob, acceptorsiteprob;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<exon-intron_info xmlns=\"http://www.genomethreader.org/"
"GTH_output/PGL_module/predicted_gene_location/"
"AGS_information/exon-intron_info/\">\n");
indentlevel++;
for (i = 0; i < gt_array_size(ags->exons); i++) {
exon = (GthExonAGS*) gt_array_get(ags->exons, i);
leftexonborder = exon->range.start;
rightexonborder = exon->range.end;
exonlength = rightexonborder - leftexonborder + 1;
exonscore = exon->score;
if (i > 0) {
rightintronborder = leftexonborder - 1;
intronlength = rightintronborder - leftintronborder + 1;
splicesiteprob = (GthSpliceSiteProb*)
gt_array_get(ags->splicesiteprobs, i-1);
donorsiteprob = splicesiteprob->donorsiteprob;
acceptorsiteprob = splicesiteprob->acceptorsiteprob;
/* output intron */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<intron i_serial=\"%lu\" don_prob=\"%.3f\" "
"acc_prob=\"%.3f\">\n", i - 1 + OUTPUTOFFSET,
donorsiteprob, acceptorsiteprob);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<gDNA_intron_boundary i_start=\"%lu\" i_stop=\"%lu\" "
"i_length=\"%lu\"/>\n",
SHOWGENPOSAGS(leftintronborder),
SHOWGENPOSAGS(rightintronborder), intronlength);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</intron>\n");
}
leftintronborder = rightexonborder + 1;
/* output exon */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon e_serial=\"%lu\" e_score=\"%.3f\">\n",
i + OUTPUTOFFSET, exonscore);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<gDNA_exon_boundary e_start=\"%lu\" e_stop=\"%lu\" "
"e_length=\"%lu\"/>\n", SHOWGENPOSAGS(leftexonborder),
SHOWGENPOSAGS(rightexonborder), exonlength);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon>\n");
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon-intron_info>\n");
}
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]);
}
static void xml_final_sa_visitor_preface(GthSAVisitor *sa_visitor)
{
GthXMLFinalSAVisitor *visitor = xml_final_sa_visitor_cast(sa_visitor);
gth_indent(visitor->outfp, visitor->indentlevel);
gt_file_xprintf(visitor->outfp, "<alignment_module>\n");
}
static void xml_showalignmentheader(GthSA *sa,
unsigned long minintronlength,
unsigned int indentlevel, GtFile *outfp)
{
unsigned long i, leftreferenceexonborder, rightreferenceexonborder,
referenceexonlength;
GthDbl exonscore, donorsitescore, acceptorsitescore;
GthFlt donorsiteprobability, acceptorsiteprobability;
Exoninfo *exoninfo;
Introninfo *introninfo;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<predicted_gene_structure>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon-intron_info>\n");
indentlevel++;
for (i = 0; i < gth_sa_num_of_exons(sa); i++) {
exoninfo = gth_sa_get_exon(sa, i);
leftreferenceexonborder = exoninfo->leftreferenceexonborder;
rightreferenceexonborder = exoninfo->rightreferenceexonborder;
referenceexonlength = rightreferenceexonborder
- leftreferenceexonborder + 1;
exonscore = exoninfo->exonscore;
if (i > 0) {
introninfo = gth_sa_get_intron(sa, i-1);
donorsiteprobability = introninfo->donorsiteprobability;
donorsitescore = introninfo->donorsitescore;
acceptorsiteprobability = introninfo->acceptorsiteprobability;
acceptorsitescore = introninfo->acceptorsitescore;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<intron i_serial=\"%lu\">\n",
i - 1 + OUTPUTOFFSET);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<gDNA_intron_boundary i_start=\"%lu\" i_stop=\"%lu\" "
"i_length=\"%lu\">\n",
gth_sa_left_intron_border(sa, i-1),
gth_sa_right_intron_border(sa, i-1),
gth_sa_intron_length(sa, i-1));
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<donor d_prob=\"%.3f\"", donorsiteprobability);
if (gth_sa_alphatype(sa) == DNA_ALPHA)
gt_file_xprintf(outfp, " d_score=\"%.2f\"", donorsitescore);
gt_file_xprintf(outfp, "/>\n");
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<acceptor a_prob=\"%.3f\"",
acceptorsiteprobability);
if (gth_sa_alphatype(sa) == DNA_ALPHA)
gt_file_xprintf(outfp, " a_score=\"%.2f\"", acceptorsitescore);
gt_file_xprintf(outfp, "/>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</gDNA_intron_boundary>\n");
/* if the intron is shorter or equal than the minimal intron length an
additional tag is shown */
if (gth_sa_intron_length(sa, i-1) <= minintronlength) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<shorter_than_min_intron_len/>\n");
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</intron>\n");
}
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon e_serial=\"%lu\">\n", i + OUTPUTOFFSET);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<gDNA_exon_boundary g_start=\"%lu\" g_stop="
"\"%lu\" g_length=\"%lu\"/>\n",
gth_sa_left_genomic_exon_border(sa, i),
gth_sa_right_genomic_exon_border(sa, i),
gth_sa_genomic_exon_length(sa, i));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<reference_exon_boundary r_type=\"%s\" r_start=\"%lu\" "
"r_stop=\"%lu\" r_length=\"%lu\" r_score=\"%5.3f\"/>\n",
gth_sa_alphastring(sa),
leftreferenceexonborder + OUTPUTOFFSET ,
rightreferenceexonborder + OUTPUTOFFSET ,
referenceexonlength, exonscore);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon>\n");
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon-intron_info>\n");
/* showing PPA line (if an poly-A tail was determined) */
if (gth_sa_alphatype(sa) == DNA_ALPHA)
xml_showppaline(sa, indentlevel, outfp);
/* showing MATCH line */
xml_showmatchline(sa, indentlevel, outfp);
/* showing PGS line */
xml_showpgsline(sa, indentlevel, 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);
}
static void showalignmentcutoffs(GthSA *sa, unsigned int indentlevel,
GtFile *outfp)
{
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<cutoffs>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<cutoffsstart>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomiccutoff>"GT_WU"</genomiccutoff>\n",
gth_sa_genomiccutoff_start(sa));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<referencecutoff>"GT_WU"</referencecutoff>\n",
gth_sa_referencecutoff_start(sa));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<eopcutoff>"GT_WU"</eopcutoff>\n",
gth_sa_eopcutoff_start(sa));
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</cutoffsstart>\n");
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<cutoffsend>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomiccutoff>"GT_WU"</genomiccutoff>\n",
gth_sa_genomiccutoff_end(sa));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<referencecutoff>"GT_WU"</referencecutoff>\n",
gth_sa_referencecutoff_end(sa));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<eopcutoff>"GT_WU"</eopcutoff>\n",
gth_sa_eopcutoff_end(sa));
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</cutoffsend>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</cutoffs>\n");
}
static void showtranslation(GthSplicedSeq *splicedseq,
char *frame0_in,
char *frame1_in,
char *frame2_in,
GtArray *exons,
bool gen_strand_forward,
unsigned long gen_total_length,
unsigned long gen_offset,
unsigned int indentlevel,
GthOutput *out)
{
char *dotline, *template_out, *frame0_out, *frame1_out, *frame2_out;
unsigned long i, exonseparatorwidth = strlen(EXONSEPARATORSTRING),
outlen = splicedseq->splicedseqlen +
((gt_array_size(exons) - 1) * exonseparatorwidth) +
(splicedseq->splicedseqlen / TRANSLATIONLINEWIDTH);
GtFile *outfp = out->outfp;
dotline = gt_malloc(sizeof (unsigned char) * outlen);
template_out = gt_malloc(sizeof (unsigned char) * outlen);
frame0_out = gt_malloc(sizeof (unsigned char) * outlen);
frame1_out = gt_malloc(sizeof (unsigned char) * outlen);
frame2_out = gt_malloc(sizeof (unsigned char) * outlen);
createoutputlines(dotline, template_out, frame0_out, frame1_out, frame2_out,
(char*) splicedseq->splicedseq, frame0_in, frame1_in,
frame2_in, splicedseq, exonseparatorwidth, outlen,
out->gs2out);
if (out->xmlout) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<translation>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<gDNA_template>");
for (i = 0; i < outlen; i++) {
if (template_out[i] != '\n') {
gt_file_xfputc(template_out[i], outfp);
}
}
gt_file_xprintf(outfp, "</gDNA_template>\n");
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<first_frame>");
for (i = 0; i < outlen; i++) {
if (frame0_out[i] != '\n') {
gt_file_xfputc(frame0_out[i], outfp);
}
}
gt_file_xprintf(outfp, "</first_frame>\n");
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<second_frame>");
for (i = 0; i < outlen; i++) {
if (frame1_out[i] != '\n') {
gt_file_xfputc(frame1_out[i], outfp);
}
}
gt_file_xprintf(outfp, "</second_frame>\n");
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<third_frame>");
for (i = 0; i < outlen; i++) {
if (frame2_out[i] != '\n') {
gt_file_xfputc(frame2_out[i], outfp);
}
}
gt_file_xprintf(outfp, "</third_frame>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</translation>\n");
}
else {
showoutputlines(dotline, template_out, frame0_out, frame1_out, frame2_out,
outlen, gen_strand_forward, gen_total_length,
gen_offset, splicedseq->positionmapping, out);
}
gt_free(dotline);
gt_free(template_out);
gt_free(frame0_out);
gt_free(frame1_out);
gt_free(frame2_out);
}
