void gth_bssm_param_echo(const GthBSSMParam *bssm_param, FILE *outfp)
{
gt_assert(bssm_param && outfp);
fprintf(outfp, "BSSMPARAMVERSION is %u\n\n", bssm_param->version_num);
fprintf(outfp, "Is the GT donor model set? -> %s\n",
GTH_SHOWBOOL(bssm_param->gt_donor_model_set));
fprintf(outfp, "Is the GC donor model set? -> %s\n\n",
GTH_SHOWBOOL(bssm_param->gc_donor_model_set));
fprintf(outfp, "Is the AG acceptor model set? -> %s\n\n",
GTH_SHOWBOOL(bssm_param->ag_acceptor_model_set));
if (gth_bssm_param_is_seven_class(bssm_param)) {
if (bssm_param->gt_donor_model_set) {
fprintf(outfp, "reporting GT donor model parameterization");
bssm_model_echo(&bssm_param->gt_donor_model, outfp);
}
if (bssm_param->gc_donor_model_set) {
fprintf(outfp, "reporting GC donor model parameterization");
bssm_model_echo(&bssm_param->gc_donor_model, outfp);
}
if (bssm_param->ag_acceptor_model_set) {
fprintf(outfp, "reporting AG acceptor model parameterization");
bssm_model_echo(&bssm_param->ag_acceptor_model, outfp);
}
}
else {
fprintf(outfp,
"Cannot report model parameterization for two-class BSSMs.\n");
}
}
void gth_bssm_param_show_info(const GthBSSMParam *bssm_param, GtFile *outfp)
{
#define SEVENCLASSSTRING "seven-class"
#define TWOCLASSSTRING "two-class"
#define PRINT_CLASS_STRING(MODEL) \
if (bssm_param->MODEL##_model_set) \
{ \
gt_file_xprintf(outfp, " (%s)", \
bssm_param->MODEL##_model.hypothesis_num == HYPOTHESIS7 \
? SEVENCLASSSTRING : TWOCLASSSTRING); \
} \
gt_file_xfputc('\n', outfp);
gt_file_xprintf(outfp,
"%c the specified BSSM parameter file contains the following "
"models:\n", COMMENTCHAR);
gt_file_xprintf(outfp, "%c GT donor sites = %s", COMMENTCHAR,
GTH_SHOWBOOL(bssm_param->gt_donor_model_set));
PRINT_CLASS_STRING(gt_donor);
gt_file_xprintf(outfp, "%c GC donor sites = %s", COMMENTCHAR,
GTH_SHOWBOOL(bssm_param->gc_donor_model_set));
PRINT_CLASS_STRING(gc_donor);
gt_file_xprintf(outfp, "%c AG acceptor sites= %s", COMMENTCHAR,
GTH_SHOWBOOL(bssm_param->ag_acceptor_model_set));
PRINT_CLASS_STRING(ag_acceptor);
}
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");
}
