void gth_sa_set(GthSA *sa, GthAlphatype ref_alphatype,
GtUword gen_dp_start, GtUword gen_dp_length)
{
gth_backtrace_path_set_gen_dp_start(sa->backtrace_path, gen_dp_start);
gth_backtrace_path_set_gen_dp_length(sa->backtrace_path, gen_dp_length);
gth_sa_set_score(sa, 0.0);
gth_sa_set_coverage(sa, 0.0);
gth_sa_set_highest_cov(sa, true);
gth_sa_set_cumlen_scored_exons(sa, 0);
/* reset edit operations */
gth_backtrace_path_reset(sa->backtrace_path);
gth_backtrace_path_set_alphatype(sa->backtrace_path, ref_alphatype);
/* reset arrays */
gt_array_reset(sa->exons);
gt_array_reset(sa->introns);
}
void gth_compute_scores(GthSA *sa,
bool proteineop,
GthDPParam *dp_param,
void *dp_options_est,
const unsigned char *gen_seq_tran,
const unsigned char *ref_seq_tran,
const unsigned char *ref_seq_orig,
const GtTransTable *transtable,
unsigned long gen_dp_start,
unsigned long scoreminexonlen,
bool introncutout,
bool gs2out,
GthSplicedSeq *spliced_seq,
unsigned long ref_dp_length,
GtAlphabet *gen_alphabet,
GtAlphabet *ref_alphabet,
GthDPScoresProtein *dp_scores_protein)
{
Traversealignmentfunctions travfunctions;
Traversealignmentstate travstate;
Computebordersandscoresdata data;
GthFlt score, coverageofgenomicsegment, coverageofreferencesegment;
gt_assert(!gth_sa_num_of_exons(sa));
gt_assert(!gth_sa_num_of_introns(sa));
travfunctions.processmismatch = computescoresprocmismatch;
travfunctions.processdeletion = computescoresprocdeletion;
travfunctions.processinsertion = computebordersandscoresprocinsertion;
travfunctions.processmatch = computebordersandscoresprocmatch;
travfunctions.processintron = computebordersandscoresprocintron;
travfunctions.breakcondition = NULL;
/* additional functions for protein edit operations */
travfunctions.processintron_with_1_base_left =
computebordersandscoresprocintron;
travfunctions.processintron_with_2_bases_left =
computebordersandscoresprocintron;
travfunctions.processmismatch_with_1_gap =
computescoresprocmismatchordeletionwithgap;
travfunctions.processmismatch_with_2_gaps =
computescoresprocmismatchordeletionwithgap;
travfunctions.processdeletion_with_1_gap =
computescoresprocmismatchordeletionwithgap;
travfunctions.processdeletion_with_2_gaps =
computescoresprocmismatchordeletionwithgap;
travstate.proteineop = proteineop;
travstate.processing_intron_with_1_base_left = false;
travstate.processing_intron_with_2_bases_left = false;
travstate.alignment = gth_sa_get_editoperations(sa);
travstate.alignmentlength = gth_sa_get_editoperations_length(sa);
travstate.eopptr = travstate.alignment + travstate.alignmentlength - 1;
travstate.genomicptr = gth_sa_genomiccutoff_start(sa);
travstate.referenceptr = gth_sa_referencecutoff_start(sa);
if (travstate.alignmentlength <= 0) {
/* in this case the alignmentscore is set to 0, which leads to discarding
this alignment later */
gth_sa_set_score(sa, 0.0);
return;
}
/* editoperations contain no zero base exons */
gt_assert(gth_sa_contains_no_zero_base_exons(sa));
/* editoperations contain no leading or terminal introns or insertions */
gt_assert(containsnoleadingorterminalintronsorinsertions(travstate.alignment,
travstate
.alignmentlength,
proteineop));
/* sum of edit operations equals referencelength */
gt_assert(gt_eops_equal_referencelength(travstate.alignment,
travstate.alignmentlength,
ref_dp_length
- gth_sa_referencecutoff_start(sa)
- gth_sa_referencecutoff_end(sa),
proteineop));
data.proteineop = proteineop;
data.newexon = true;
data.newintron = true;
data.firstexon = true;
data.introncutout = introncutout;
data.gs2out = gs2out;
data.spliced_seq = spliced_seq;
data.singleexonweight = (GthFlt) 0.0;
data.maxsingleexonweight = (GthFlt) 0.0;
data.overallexonweight = (GthFlt) 0.0;
data.maxoverallexonweight = (GthFlt) 0.0;
data.cumulativelengthofscoredexons = 0;
data.exon.leftgenomicexonborder = GT_UNDEF_ULONG;
data.exon.rightgenomicexonborder = GT_UNDEF_ULONG;
data.exon.leftreferenceexonborder = GT_UNDEF_ULONG;
data.exon.rightreferenceexonborder = GT_UNDEF_ULONG;
data.exon.exonscore = GTH_UNDEF_GTHDBL;
data.intron.donorsiteprobability = GTH_UNDEF_GTHFLT;
data.intron.acceptorsiteprobability = GTH_UNDEF_GTHFLT;
data.intron.donorsitescore = GTH_UNDEF_GTHDBL;
data.intron.acceptorsitescore = GTH_UNDEF_GTHDBL;
data.sa = sa;
data.dp_param = dp_param;
data.dp_options_est = dp_options_est;
data.gen_seq_tran = gen_seq_tran;
data.ref_seq_tran = ref_seq_tran;
data.ref_seq_orig = ref_seq_orig;
data.transtable = transtable;
data.gen_dp_start = gen_dp_start;
data.scoreminexonlen = scoreminexonlen;
data.ref_dp_length = ref_dp_length;
data.gen_alphabet = gen_alphabet;
data.gen_alphabet_characters = gen_alphabet
? gt_alphabet_characters(gen_alphabet)
: NULL;
data.dp_scores_protein = dp_scores_protein;
gthtraversealignment(true, &travstate, proteineop, &data, &travfunctions);
/* this is for saving the last exon */
evalnewintronifpossible(proteineop, &data.newexon, &data.newintron, true,
data.introncutout, data.gs2out, data.spliced_seq,
&data.exon, &data.intron, &data.singleexonweight,
&data.maxsingleexonweight, &data.overallexonweight,
&data.maxoverallexonweight,
&data.cumulativelengthofscoredexons, sa, &travstate,
gen_alphabet, data.dp_param, data.dp_options_est,
data.gen_seq_tran, data.ref_seq_tran,
data.gen_dp_start, data.scoreminexonlen);
/* saving the scores for the whole alignment */
if (data.maxoverallexonweight > 0.0) {
score = data.overallexonweight / data.maxoverallexonweight;
/* XXX: the way the alignmentscore is computed, it is possible to get a
score > 1.0. Since we don't want this, we cap it */
if (score > 1.0)
score = 1.0;
}
else
score = 0.0;
gth_sa_set_score(sa, score);
gth_sa_set_cumlen_scored_exons(sa, data.cumulativelengthofscoredexons);
/* fraction of the gen_dp_length which is scored/weighted */
coverageofgenomicsegment = (GthFlt) data.cumulativelengthofscoredexons /
(GthFlt) gth_sa_gen_dp_length(sa);
/* coverage of genomic segment is valid value */
gt_assert(coverageofgenomicsegment >= 0.0 && coverageofgenomicsegment <= 1.0);
/* fraction of the referencelength which is scored/weighted */
coverageofreferencesegment = (GthFlt) data.cumulativelengthofscoredexons /
(GthFlt) ((proteineop ? GT_CODON_LENGTH : 1) *
gth_sa_ref_total_length(sa));
if (coverageofgenomicsegment > coverageofreferencesegment) {
gth_sa_set_coverage(sa, coverageofgenomicsegment);
gth_sa_set_highest_cov(sa, true);
}
else {
gth_sa_set_coverage(sa, coverageofreferencesegment);
gth_sa_set_highest_cov(sa, false);
}
/* test the assumption that the coverage is never larger then the default */
gt_assert(gth_sa_coverage(sa) <= GTH_DEFAULT_MAX_COVERAGE);
/* compute poly(A) tail position */
gth_sa_calc_polyAtailpos(sa, ref_seq_tran, ref_alphabet);
/* determined exons are forward and consecutive */
gt_assert(gth_sa_exons_are_forward_and_consecutive(sa));
}
static void end_element_handler(void *info, const XML_Char *name)
{
Parseinfo *parseinfo = (Parseinfo*) info;
GthSA *sa = parseinfo->currentSA;
GtUword datalength;
double retdouble;
GtWord ret;
char *data;
/* save data and data length */
data = gt_str_get(parseinfo->databuf);
datalength = gt_str_length(parseinfo->databuf);
/* perform actions depending on end tag */
if (strcmp(name, SPLICEDALIGNMENT_TAG) == 0) {
/* before we store the spliced alignment we have to reverse its edit
operations */
gt_assert(sa && gth_sa_backtrace_path(sa));
gth_backtrace_path_reverse(gth_sa_backtrace_path(sa));
/* ensure that before an intron which is not in phase the edit operation
has length 1 (only for protein spliced alignments) */
gth_backtrace_path_ensure_length_1_before_introns(
gth_sa_backtrace_path(sa));
if (parseinfo->saprocessfunc(parseinfo->data , sa,
parseinfo->outputfilename, parseinfo->err)) {
/* XXX */
fprintf(stderr, "error: %s\n", gt_error_get(parseinfo->err));
exit(EXIT_FAILURE);
}
/* reset current spliced alignment */
parseinfo->currentSA = NULL;
}
else if (strcmp(name, REFERENCEALPHATYPE_TAG) == 0) {
if (strcmp(data, "DNA_ALPHA") == 0)
gth_sa_set_alphatype(sa, DNA_ALPHA);
else if (strcmp(data, "PROTEIN_ALPHA") == 0) {
gth_sa_set_alphatype(sa, PROTEIN_ALPHA);
}
else {
ILLEGAL_DATA;
}
}
else if (strcmp(name, DNA_EOP_TYPE_TAG) == 0) {
if (strcmp(data, "match") == 0)
parseinfo->eoptype = EOP_TYPE_MATCH;
else if (strcmp(data, "deletion") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION;
else if (strcmp(data, "insertion") == 0)
parseinfo->eoptype = EOP_TYPE_INSERTION;
else if (strcmp(data, "mismatch") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH;
else if (strcmp(data, "intron") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON;
else {
ILLEGAL_DATA;
}
}
else if (strcmp(name, DNA_EOP_LENGTH_TAG) == 0) {
SCANUINT;
gth_backtrace_path_add_eop(gth_sa_backtrace_path(sa), parseinfo->eoptype,
ret);
}
else if (strcmp(name, PROTEIN_EOP_TYPE_TAG) == 0) {
if (strcmp(data, "match") == 0)
parseinfo->eoptype = EOP_TYPE_MATCH;
else if (strcmp(data, "deletion") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION;
else if (strcmp(data, "insertion") == 0)
parseinfo->eoptype = EOP_TYPE_INSERTION;
else if (strcmp(data, "mismatch") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH;
else if (strcmp(data, "intron") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON;
else if (strcmp(data, "mismatch_with_1_gap") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH_WITH_1_GAP;
else if (strcmp(data, "mismatch_with_2_gaps") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH_WITH_2_GAPS;
else if (strcmp(data, "deletion_with_1_gap") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION_WITH_1_GAP;
else if (strcmp(data, "deletion_with_2_gaps") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION_WITH_2_GAPS;
else if (strcmp(data, "intron_with_1_base_left") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON_WITH_1_BASE_LEFT;
else if (strcmp(data, "intron_with_2_bases_left") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON_WITH_2_BASES_LEFT;
else {
ILLEGAL_DATA;
}
}
else if (strcmp(name, PROTEIN_EOP_LENGTH_TAG) == 0) {
SCANUINT;
gth_backtrace_path_add_eop(gth_sa_backtrace_path(sa), parseinfo->eoptype,
ret);
}
else if (strcmp(name, INDELCOUNT_TAG) == 0) {
SCANUINT;
/* ignore indelcount, gets recomputed anyway */
}
else if (strcmp(name, GENOMICLENGTHDP_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_dp_length(sa, ret);
}
else if (strcmp(name, GENOMICLENGTHTOTAL_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_total_length(sa, ret);
}
else if (strcmp(name, GENOMICOFFSET_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_offset(sa, ret);
}
else if (strcmp(name, REFERENCELENGTH_TAG) == 0) {
SCANUINT;
gth_sa_set_ref_total_length(sa, ret);
}
else if (strcmp(name, DPSTARTPOS_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_dp_start(sa, ret);
}
else if (strcmp(name, DPENDPOS_TAG) == 0) {
SCANUINT;
/* ignore DP end pos, gets recomputed from gen_dp_length anyway */
gt_assert(gth_sa_gen_dp_end(sa) == ret);
}
else if (strcmp(name, GENOMICFILENAME_TAG) == 0) {
/* save genomic file name */
gt_str_append_cstr_nt(parseinfo->genomicfilename, data, datalength);
}
else if (strcmp(name, GENOMICFILEHASH_TAG) == 0) {
gth_sa_set_gen_file_num(sa, process_file(parseinfo->input,
gt_str_get(parseinfo->genomicfilename), data, false,
UNDEF_ALPHA));
/* reset genomic filename */
gt_str_reset(parseinfo->genomicfilename);
}
else if (strcmp(name, GENOMICSEQNUM_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_seq_num(sa, ret);
}
else if (strcmp(name, REFERENCEFILENAME_TAG) == 0) {
/* save reference file name */
gt_str_append_cstr_nt(parseinfo->referencefilename, data, datalength);
}
else if (strcmp(name, REFERENCEFILEHASH_TAG) == 0) {
gth_sa_set_ref_file_num(sa, process_file(parseinfo->input,
gt_str_get(parseinfo->referencefilename),
data, true,
gth_sa_alphatype(sa)));
/* reset reference filename */
gt_str_reset(parseinfo->referencefilename);
}
else if (strcmp(name, REFERENCESEQNUM_TAG) == 0) {
SCANUINT;
gth_sa_set_ref_seq_num(sa, ret);
}
else if (strcmp(name, GENOMICID_TAG) == 0)
gth_sa_set_gen_id(sa, data);
else if (strcmp(name, REFERENCEID_TAG) == 0)
gth_sa_set_ref_id(sa, data);
else if (strcmp(name, GENOMICSTRANDISFORWARD_TAG) == 0)
gth_sa_set_gen_strand(sa, parse_boolean(data, parseinfo));
else if (strcmp(name, REFERENCESTRANDISFORWARD_TAG) == 0)
gth_sa_set_ref_strand(sa, parse_boolean(data, parseinfo));
else if (strcmp(name, GENOMICCUTOFF_TAG) == 0) {
SCANUINT;
parseinfo->cutoffs.genomiccutoff = ret;
}
else if (strcmp(name, REFERENCECUTOFF_TAG) == 0) {
SCANUINT;
parseinfo->cutoffs.referencecutoff = ret;
}
else if (strcmp(name, EOPCUTOFF_TAG) == 0) {
SCANUINT;
parseinfo->cutoffs.eopcutoff = ret;
}
else if (strcmp(name, CUTOFFSSTART_TAG) == 0)
gth_sa_set_cutoffs_start(sa, &parseinfo->cutoffs);
else if (strcmp(name, CUTOFFSEND_TAG) == 0)
gth_sa_set_cutoffs_end(sa, &parseinfo->cutoffs);
else if (strcmp(name, LEFTGENOMICEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.leftgenomicexonborder = ret;
}
else if (strcmp(name, RIGHTGENOMICEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.rightgenomicexonborder = ret;
}
else if (strcmp(name, LEFTREFERENCEEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.leftreferenceexonborder = ret;
}
else if (strcmp(name, RIGHTREFERENCEEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.rightreferenceexonborder = ret;
}
else if (strcmp(name, EXONSCORE_TAG) == 0) {
SCANDOUBLE;
parseinfo->exoninfo.exonscore = retdouble;
}
else if (strcmp(name, EXONINFO_TAG) == 0)
gth_sa_add_exon(sa, &parseinfo->exoninfo);
else if (strcmp(name, DONORSITEPROBABILITY_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.donorsiteprobability = (GthFlt) retdouble;
}
else if (strcmp(name, ACCEPTORSITEPROBABILITY_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.acceptorsiteprobability = (GthFlt) retdouble;
}
else if (strcmp(name, DONORSITESCORE_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.donorsitescore = retdouble;
}
else if (strcmp(name, ACCEPTORSITESCORE_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.acceptorsitescore = retdouble;
}
else if (strcmp(name, INTRONINFO_TAG) == 0)
gth_sa_add_intron(sa, &parseinfo->introninfo);
else if (strcmp(name, POLYASTART_TAG) == 0) {
SCANUINT;
gth_sa_set_polyAtail_start(sa, ret);
}
else if (strcmp(name, POLYAEND_TAG) == 0) {
SCANUINT;
gth_sa_set_polyAtail_stop(sa, ret);
}
else if (strcmp(name, ALIGNMENTSCORE_TAG) == 0) {
SCANDOUBLE;
gth_sa_set_score(sa, retdouble);
}
else if (strcmp(name, COVERAGE_TAG) == 0) {
SCANDOUBLE;
gth_sa_set_coverage(sa, retdouble);
}
else if (strcmp(name, COVERAGEOFGENOMICSEGMENTISHIGHEST_TAG) == 0) {
gth_sa_set_highest_cov(sa, parse_boolean(data, parseinfo));
}
else if (strcmp(name, CUMULATIVELENGTHOFSCOREDEXONS_TAG) == 0) {
SCANUINT;
gth_sa_set_cumlen_scored_exons(sa, ret);
}
}
