static VALUE problem_alloc(VALUE cls) {
struct svm_problem *n;
n = problem_new();
if(n == NULL)
rb_raise(rb_eNoMemError, "Not enough memory for allocating Libsvm::Problem.");
return Data_Wrap_Struct(cls, 0, problem_free, n);
}
void
solver_problems_iterate( Solver *solver, Request *t, int (*callback)(Problem *p, void *user_data), void *user_data )
{
Id problem = 0;
if (!callback)
return; /* no use to iterate without callback */
while ((problem = solver_next_problem( solver, problem )) != 0)
{
Problem *p = problem_new( solver, t, problem );
if (callback( p, user_data ) )
break;
}
}
/* scans a cds for gaps. Returns CLN_GAPS, NOVRLP_CLN_GAPS, NO_GAPS,
or FSHIFT_BAD; doesn't try to check for compensatory indels, which
is more complicated (this is left for the special-purpose function
below) */
int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {
int msa_start = feat->start - 1;
int msa_end = feat->end - 1;
int i, j;
int near_boundary = 0;
cds_gap_type retval = NGAPS;
List *gaps = lst_new_ptr(10);
for (j = 0; retval != FSHIFT_BAD && j < msa->nseqs; j++) {
for (i = msa_start; i <= msa_end; i++) {
if (ss_get_char_pos(msa, i, j, 0) == GAP_CHAR) {
int gap_start, gap_end;
struct gap *g;
for (gap_start = i-1; gap_start >= msa_start &&
ss_get_char_pos(msa, gap_start, j, 0) == GAP_CHAR; gap_start--);
gap_start++; /* inclusive */
for (gap_end = i+1; gap_end <= msa_end &&
ss_get_char_pos(msa, gap_end, j, 0) == GAP_CHAR; gap_end++);
gap_end--; /* inclusive */
if ((gap_end - gap_start + 1) % 3 != 0) {
retval = FSHIFT_BAD;
*problem = problem_new(feat, FSHIFT, gap_start, gap_end);
(*problem)->cds_gap = FSHIFT_BAD;
break;
}
/* note whether gaps occur near a cds boundary (within 3 sites) */
if (gap_start <= msa_start + 3 || gap_end >= msa_end - 3)
near_boundary = 1;
if (retval == NGAPS) retval = CLN_GAPS;
g = smalloc(sizeof(struct gap));
g->start = gap_start;
g->end = gap_end;
lst_push_ptr(gaps, g);
i = gap_end;
}
}
}
if (retval == CLN_GAPS) { /* now check for overlaps */
lst_qsort(gaps, gap_compare);
retval = NOVRLP_CLN_GAPS;
for (i = 1; i < lst_size(gaps); i++) {
struct gap *g1 = lst_get_ptr(gaps, i-1);
struct gap *g2 = lst_get_ptr(gaps, i);
if (g2->start <= g1->end &&
(g2->start != g1->start || g2->end != g1->end)) {
retval = CLN_GAPS;
break;
}
}
if (retval == NOVRLP_CLN_GAPS && near_boundary)
retval = CLN_GAPS; /* note that the boundary criterion is
being confounded with the overlap
criterion. Doesn't seem worth
fixing at the moment ... */
}
for (i = 0; i < lst_size(gaps); i++) sfree(lst_get_ptr(gaps, i));
lst_free(gaps);
return retval;
}
/* create a new problem, and add to the list */
Problem *problem_add(List *problems, GFF_Feature *feat, status_type status,
int start, int end) {
Problem *p = problem_new(feat, status, start, end);
lst_push_ptr(problems, p);
return p;
}
