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));
}
bool gth_sa_is_valid(const GthSA *sa)
{
gt_assert(sa);
return gth_backtrace_path_is_valid(sa->backtrace_path);
}
