void gth_backtrace_path_remove_zero_base_exons(GthBacktracePath *bp,
GthStat *stat)
{
gt_assert(bp);
gt_remove_zero_base_exons(gth_backtrace_path_get(bp),
gth_backtrace_path_length(bp), stat);
}
bool gth_backtrace_path_contains_no_zero_base_exons(const GthBacktracePath *bp)
{
gt_assert(bp);
return contains_no_zero_base_exons(gth_backtrace_path_get(bp) +
bp->cutoffs.end.eopcutoff,
gth_backtrace_path_length(bp) -
bp->cutoffs.start.eopcutoff -
bp->cutoffs.end.eopcutoff);
}
void gth_backtrace_path_show(const GthBacktracePath *bp, bool xmlout,
unsigned int indentlevel, GtFile *outfp)
{
gt_assert(bp);
gt_assert(bp->alphatype == DNA_ALPHA || bp->alphatype == PROTEIN_ALPHA);
gt_editoperation_show(gth_backtrace_path_get(bp),
gth_backtrace_path_length(bp),
bp->alphatype == PROTEIN_ALPHA, xmlout, indentlevel,
outfp);
}
GthPathWalker* gth_path_walker_new(const GthBacktracePath *bp, bool forward)
{
GthPathWalker *pw;
gt_assert(bp);
gt_assert(forward); /* XXX: implement reverse walking */
pw = gt_calloc(1, sizeof *pw);
pw->forward = forward;
pw->proteineop = gth_backtrace_path_alphatype(bp) == PROTEIN_ALPHA;
pw->alignment = gth_backtrace_path_get(bp);
pw->alignmentlength = gth_backtrace_path_length(bp);
pw->eopptr = pw->alignment + pw->alignmentlength - 1;
pw->last_eop_type = NUM_OF_EOP_TYPES;
return pw;
}
static void determine_cutoffs(GthBacktracePath *bp,
GthCutoffmode leadcutoffsmode,
GthCutoffmode termcutoffsmode,
unsigned long cutoffsminexonlen)
{
Traversealignmentfunctions travfunctions;
Traversealignmentstate travstate;
Relaxedcutoffsdata relaxedcutoffsdata;
Strictcutoffsdata strictcutoffsdata;
Minimalcutoffsdata minimalcutoffsdata;
bool proteineop = bp->alphatype == PROTEIN_ALPHA;
/* sum of edit operations equals referencelength (before cutoffs)", */
gt_assert(gth_backtrace_path_is_valid(bp));
/* setting the traverse alignment state */
travstate.proteineop = proteineop;
travstate.processing_intron_with_1_base_left = false;
travstate.processing_intron_with_2_bases_left = false;
travstate.alignment = gth_backtrace_path_get(bp);
travstate.alignmentlength = gth_backtrace_path_length(bp);
travstate.eopptr = travstate.alignment +
travstate.alignmentlength - 1;
travstate.genomicptr = 0;
travstate.referenceptr = 0;
/* cutting of leading indels in the sequences */
switch (leadcutoffsmode) {
case RELAXED:
gt_initRelaxedcutoffsTravfunctions(&travfunctions);
gt_initRelaxedcutoffsdata(&relaxedcutoffsdata, &bp->cutoffs.start);
gthtraversealignment(true, &travstate, proteineop, &relaxedcutoffsdata,
&travfunctions);
break;
case STRICT:
gt_initStrictcutoffsTravfunctions(&travfunctions);
gt_initStrictcutoffsdata(&strictcutoffsdata, &bp->cutoffs.start,
cutoffsminexonlen);
gthtraversealignment(true , &travstate , proteineop, &strictcutoffsdata,
&travfunctions);
break;
case MINIMAL:
gt_initMinimalcutoffsTravfunctions(&travfunctions);
gt_initMinimalcutoffsdata(&minimalcutoffsdata, &bp->cutoffs.start);
gthtraversealignment(true, &travstate, proteineop, &minimalcutoffsdata,
&travfunctions);
break;
default: gt_assert(0);
}
/* resetting the traverse alignment state */
travstate.processing_intron_with_1_base_left = false;
travstate.processing_intron_with_2_bases_left = false;
travstate.eopptr = gth_backtrace_path_get(bp);
travstate.genomicptr = 0;
travstate.referenceptr = 0;
/* cutting of terminal indels in the sequences */
switch (termcutoffsmode) {
case RELAXED:
gt_initRelaxedcutoffsTravfunctions(&travfunctions);
gt_initRelaxedcutoffsdata(&relaxedcutoffsdata, &bp->cutoffs.end);
gthtraversealignment(false, &travstate, proteineop, &relaxedcutoffsdata,
&travfunctions);
break;
case STRICT:
gt_initStrictcutoffsTravfunctions(&travfunctions);
gt_initStrictcutoffsdata(&strictcutoffsdata, &bp->cutoffs.end,
cutoffsminexonlen);
gthtraversealignment(false, &travstate, proteineop, &strictcutoffsdata,
&travfunctions);
break;
case MINIMAL:
gt_initMinimalcutoffsTravfunctions(&travfunctions);
gt_initMinimalcutoffsdata(&minimalcutoffsdata, &bp->cutoffs.end);
gthtraversealignment(false, &travstate, proteineop, &minimalcutoffsdata,
&travfunctions);
break;
default: gt_assert(0);
}
/* sum of edit operations equals referencelength (after cutoffs) */
gt_assert(gth_backtrace_path_is_valid(bp));
}
GtUword gth_sa_get_editoperations_length(const GthSA *sa)
{
gt_assert(sa);
return gth_backtrace_path_length(sa->backtrace_path);
}
bool gth_sas_are_equal(const GthSA *saA, const GthSA *saB)
{
Exoninfo *exoninfoA, *exoninfoB;
Introninfo *introninfoA, *introninfoB;
GtUword i;
/* compare element 0 */
if (gth_sa_alphatype(saA) != gth_sa_alphatype(saB))
return false;
/* compare element 1 */
if (gth_backtrace_path_length(saA->backtrace_path) !=
gth_backtrace_path_length(saB->backtrace_path)) {
return false;
}
for (i = 0; i < gth_backtrace_path_length(saA->backtrace_path); i++) {
if (((Editoperation*) gth_backtrace_path_get(saA->backtrace_path))[i] !=
((Editoperation*) gth_backtrace_path_get(saB->backtrace_path))[i]) {
return false;
}
}
/* element 2 has been removed (indelcount) */
/* compare element 3 */
if (gth_sa_gen_dp_length(saA) != gth_sa_gen_dp_length(saB))
return false;
/* compare element 4 */
if (saA->gen_total_length != saB->gen_total_length)
return false;
/* compare element 5 */
if (saA->gen_offset != saB->gen_offset)
return false;
/* compare element 6 */
if (gth_sa_ref_total_length(saA) != gth_sa_ref_total_length(saB))
return false;
/* compare element 7 */
if (gth_sa_gen_dp_start(saA) != gth_sa_gen_dp_start(saB))
return false;
/* element 8 has been removed (gen_dp_end) */
/* compare element 9 */
if (saA->gen_file_num != saB->gen_file_num)
return false;
/* compare element 10 */
if (saA->gen_seq_num != saB->gen_seq_num)
return false;
/* compare element 11 */
if (saA->ref_file_num != saB->ref_file_num)
return false;
/* compare element 12 */
if (saA->ref_seq_num != saB->ref_seq_num)
return false;
/* compare element 13 */
if (gt_str_cmp(saA->gen_id, saB->gen_id))
return false;
/* compare element 14 */
if (gt_str_cmp(saA->ref_id, saB->ref_id))
return false;
/* compare element 15 */
if (saA->gen_strand_forward != saB->gen_strand_forward)
return false;
/* compare element 16 */
if (saA->ref_strand_forward != saB->ref_strand_forward)
return false;
/* compare element 17 */
if (gth_sa_genomiccutoff_start(saA) != gth_sa_genomiccutoff_start(saB))
return false;
if (gth_sa_referencecutoff_start(saA) != gth_sa_referencecutoff_start(saB))
return false;
if (gth_sa_eopcutoff_start(saA) != gth_sa_eopcutoff_start(saB))
return false;
if (gth_sa_genomiccutoff_end(saA) != gth_sa_genomiccutoff_end(saB))
return false;
if (gth_sa_referencecutoff_end(saA) != gth_sa_referencecutoff_end(saB))
return false;
if (gth_sa_eopcutoff_end(saA) != gth_sa_eopcutoff_end(saB))
return false;
/* compare element 18 */
if (gt_array_size(saA->exons) != gt_array_size(saB->exons))
return false;
for (i = 0; i < gt_array_size(saA->exons); i++) {
exoninfoA = (Exoninfo*) gt_array_get(saA->exons, i);
exoninfoB = (Exoninfo*) gt_array_get(saB->exons, i);
if (exoninfoA->leftgenomicexonborder != exoninfoB->leftgenomicexonborder)
return false;
if (exoninfoA->rightgenomicexonborder != exoninfoB->rightgenomicexonborder)
return false;
if (exoninfoA->leftreferenceexonborder !=
exoninfoB->leftreferenceexonborder) {
return false;
}
if (exoninfoA->rightreferenceexonborder !=
exoninfoB->rightreferenceexonborder) {
return false;
}
if (!gt_double_equals_double(exoninfoA->exonscore, exoninfoB->exonscore)) {
return false;
}
}
/* compare element 19 */
if (gt_array_size(saA->introns) != gt_array_size(saB->introns))
return false;
for (i = 0; i < gt_array_size(saA->introns); i++) {
introninfoA = (Introninfo*) gt_array_get(saA->introns, i);
introninfoB = (Introninfo*) gt_array_get(saB->introns, i);
if (!gt_double_equals_double(introninfoA->donorsiteprobability,
introninfoB->donorsiteprobability)) {
return false;
}
if (!gt_double_equals_double(introninfoA->acceptorsiteprobability,
introninfoB->acceptorsiteprobability)) {
return false;
}
if (!gt_double_equals_double(introninfoA->donorsitescore,
introninfoB->donorsitescore)) {
return false;
}
if (!gt_double_equals_double(introninfoA->acceptorsitescore,
introninfoB->acceptorsitescore)) {
return false;
}
}
/* compare element 20 */
if (saA->polyAtailpos.start != saB->polyAtailpos.start)
return false;
if (saA->polyAtailpos.end != saB->polyAtailpos.end)
return false;
/* compare element 21 */
if (saA->alignmentscore != saB->alignmentscore)
return false;
/* compare element 22 */
if (saA->coverage != saB->coverage)
return false;
/* compare element 23 */
if (saA->genomic_cov_is_highest != saB->genomic_cov_is_highest)
return false;
/* compare element 24 */
if (saA->cumlen_scored_exons != saB->cumlen_scored_exons)
return false;
return true;
}
