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");
}
/* 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");
}
/* The following function prints the "classic" GeneSeqer2 MATCH line */
static void showmatchline(GthSA *sa, GtFile *outfp)
{
gt_file_xprintf(outfp, "MATCH\t%s%c\t%s%c\t%5.3f\t"GT_WU"\t%5.3f\t%c\n",
gth_sa_gen_id(sa),
gth_sa_gen_strand_char(sa),
gth_sa_ref_id(sa),
gth_sa_ref_strand_char(sa),
gth_sa_score(sa),
gth_sa_cumlen_scored_exons(sa),
gth_sa_coverage(sa),
gth_sa_coverage_char(sa));
}
/*
The following function prints the "classic" GeneSeqer2 PGS line
*/
static void showpgsline(GthSA *sa, GtFile *outfp)
{
GtUword i, numofexons;
gt_assert(sa);
numofexons = gth_sa_num_of_exons(sa);
gt_file_xprintf(outfp, "PGS_%s%c_%s%c\t(",
gth_sa_gen_id(sa),
gth_sa_gen_strand_char(sa),
gth_sa_ref_id(sa),
gth_sa_ref_strand_char(sa));
for (i = 0; i < numofexons; i++) {
gt_file_xprintf(outfp, ""GT_WU" "GT_WU"",
gth_sa_left_genomic_exon_border(sa, i),
gth_sa_right_genomic_exon_border(sa, i));
if (i == numofexons - 1)
gt_file_xprintf(outfp, ")\n\n");
else
gt_file_xfputc(',', outfp);
}
}
/*
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 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 int callsahmt(bool call_dna_dp,
GthSA *sa,
bool forward,
GtUword gen_file_num,
GtUword ref_file_num,
GthChain *raw_chain,
GtUword gen_total_length,
GtUword gen_offset,
const GtRange *gen_seq_bounds,
const GtRange *gen_seq_bounds_rc,
const unsigned char *ref_seq_tran,
const unsigned char *ref_seq_orig,
GtUword ref_total_length,
GtUword ref_offset,
GthInput *input,
Introncutoutinfo *introncutoutinfo,
GthStat *stat,
GtUword chainctr,
GtUword num_of_chains,
GtUword translationtable,
bool directmatches,
bool proteinexonpenal,
GthSpliceSiteModel *splice_site_model,
GthDPOptionsCore *dp_options_core,
GthDPOptionsEST *dp_options_est,
GthDPOptionsPostpro *dp_options_postpro,
GthDNACompletePathMatrixJT dna_complete_path_matrix_jt,
GthProteinCompletePathMatrixJT
protein_complete_path_matrix_jt,
GthOutput *out)
{
int rval;
GthChain *actual_chain, *contracted_chain, *used_chain;
GtUword icdelta = introncutoutinfo->icinitialdelta,
iciterations = introncutoutinfo->iciterations;
bool useintroncutout = introncutoutinfo->introncutout;
/* initially useintron is set to the value of introncutoutinfo->introncutout,
if the automatic intron cutotu technique is acitvated it can be set to
true if an matrix allocation error (ERROR_MATRIX_ALLOCATION_FAILED) occurs
*/
gt_assert(sa);
actual_chain = gth_chain_new();
contracted_chain = gth_chain_new();
for (;;) {
/* reset actualDPrange; */
gt_array_set_size(actual_chain->forwardranges, 0);
gt_array_set_size(actual_chain->reverseranges, 0);
/* copy raw chain to actual chain */
gth_chain_copy(actual_chain, raw_chain);
/* shorten potential introns and compute spliced sequence, if the intron
cutout technique is used */
if (useintroncutout) {
/* shorten potential introns */
gth_chain_shorten_introns(actual_chain, icdelta,
introncutoutinfo->icminremintronlength,
gen_total_length, gen_offset, out->comments,
out->outfp);
}
else
gth_chain_contract(contracted_chain, actual_chain);
if (out->showverbose) {
show_matrix_calculation_status(out->showverbose, forward,
gth_sa_ref_strand_forward(sa),
useintroncutout, chainctr, num_of_chains,
icdelta, gen_file_num,
gth_input_num_of_gen_files(input),
ref_file_num,
gth_input_num_of_ref_files(input),
directmatches, out->verboseseqs,
gth_sa_gen_id(sa), gth_sa_ref_id(sa));
}
/* allocate space for DP parameter */
if (out->comments) {
gt_file_xprintf(out->outfp, "%c alloc space for DP param "
"(genomicid=%s, referenceid=%s)\n", COMMENTCHAR,
gth_sa_gen_id(sa), gth_sa_ref_id(sa));
}
used_chain = useintroncutout ? actual_chain : contracted_chain;
/* The variable 'forward' denotes the genomic strand on which the DP is
applied. */
if (forward) {
if (call_dna_dp) {
rval = gth_align_dna(sa, used_chain->forwardranges,
gth_input_current_gen_seq_tran(input),
gth_input_current_gen_seq_orig(input),
ref_seq_tran, ref_seq_orig, ref_total_length,
gth_input_current_gen_alphabet(input),
gth_input_current_ref_alphabet(input),
useintroncutout,
introncutoutinfo->autoicmaxmatrixsize,
out->showeops, out->comments, out->gs2out,
gen_seq_bounds, splice_site_model, dp_options_core,
dp_options_est, dp_options_postpro,
dna_complete_path_matrix_jt,
raw_chain->forward_jump_table, ref_offset, stat,
out->outfp);
}
else { /* call_protein_dp */
rval = gth_align_protein(sa, used_chain->forwardranges,
gth_input_current_gen_seq_tran(input),
ref_seq_tran, ref_seq_orig, ref_total_length,
gth_input_current_gen_alphabet(input),
gth_input_current_ref_alphabet(input),
input, useintroncutout,
introncutoutinfo->autoicmaxmatrixsize,
proteinexonpenal, out->showeops, out->comments,
out->gs2out, translationtable, gen_seq_bounds,
splice_site_model, dp_options_core,
dp_options_postpro,
protein_complete_path_matrix_jt,
raw_chain->forward_jump_table, ref_offset,
stat, out->outfp);
}
}
else {
/* the DP is called with the revers positions specifiers */
if (call_dna_dp) {
rval = gth_align_dna(sa, used_chain->reverseranges,
gth_input_current_gen_seq_tran_rc(input),
gth_input_current_gen_seq_orig_rc(input),
ref_seq_tran, ref_seq_orig, ref_total_length,
gth_input_current_gen_alphabet(input),
gth_input_current_ref_alphabet(input),
useintroncutout,
introncutoutinfo->autoicmaxmatrixsize,
out->showeops, out->comments, out->gs2out,
gen_seq_bounds_rc, splice_site_model,
dp_options_core, dp_options_est,
dp_options_postpro, dna_complete_path_matrix_jt,
raw_chain->reverse_jump_table, ref_offset, stat,
out->outfp);
}
else { /* call_protein_dp */
rval = gth_align_protein(sa, used_chain->reverseranges,
gth_input_current_gen_seq_tran_rc(input),
ref_seq_tran, ref_seq_orig, ref_total_length,
gth_input_current_gen_alphabet(input),
gth_input_current_ref_alphabet(input),
input, useintroncutout,
introncutoutinfo->autoicmaxmatrixsize,
proteinexonpenal, out->showeops, out->comments,
out->gs2out, translationtable, gen_seq_bounds,
splice_site_model, dp_options_core,
dp_options_postpro,
protein_complete_path_matrix_jt,
raw_chain->reverse_jump_table, ref_offset,
stat, out->outfp);
}
}
if (rval == GTH_ERROR_DP_PARAMETER_ALLOCATION_FAILED)
return GTH_ERROR_DP_PARAMETER_ALLOCATION_FAILED;
/* handling of special error codes ERROR_CUTOUT_NOT_IN_INTRON and
ERROR_MATRIX_ALLOCATION_FAILED from DP
the only possible special error code given back by this function is
ERROR_SA_COULD_NOT_BE_DETERMINED */
#ifndef NDEBUG
if (!useintroncutout) gt_assert(rval != GTH_ERROR_CUTOUT_NOT_IN_INTRON);
#endif
if (useintroncutout && rval == GTH_ERROR_CUTOUT_NOT_IN_INTRON) {
/* the intron cutout technique failed -> increase counter */
gth_stat_increment_numofunsuccessfulintroncutoutDPs(stat);
if (--iciterations > 0) {
/* if an iterations is left, increase icdelta, decrease the remaining
iterations, and continue the while-loop */
icdelta += introncutoutinfo->icdeltaincrease;
continue;
}
else {
/* no iteration left, discard SA */
gth_stat_increment_numofundeterminedSAs(stat);
gth_chain_delete(actual_chain);
gth_chain_delete(contracted_chain);
return GTH_ERROR_SA_COULD_NOT_BE_DETERMINED;
}
}
else if (rval == GTH_ERROR_MATRIX_ALLOCATION_FAILED) {
if (introncutoutinfo->autoicmaxmatrixsize > 0 && !useintroncutout) {
/* if the automatic intron cutout technique is enabled and a ``normal''
DP returned with the matrix allocation error, set useintroncutout,
increase counter, and continue */
if (out->showverbose) {
out->showverbose("matrix allocation failed, use intron cutout "
"technique");
}
gth_stat_increment_numofautointroncutoutcalls(stat);
useintroncutout = true;
continue;
}
else {
/* otherwise increase relevant statistics, free space and return with
error */
gth_stat_increment_numoffailedmatrixallocations(stat);
gth_stat_increment_numofundeterminedSAs(stat);
gth_chain_delete(actual_chain);
gth_chain_delete(contracted_chain);
return GTH_ERROR_SA_COULD_NOT_BE_DETERMINED;
}
}
else if (rval) /* ``normal'' DP */
return -1;
break;
}
#if 0
if (out->comments) {
gt_file_xprintf(out->outfp, "%c this SA has been computed:\n", COMMENTCHAR);
gth_sa_show(sa, input, out->outfp);
}
#endif
/* free */
gth_chain_delete(actual_chain);
gth_chain_delete(contracted_chain);
return 0;
}
