std::vector<alignment_result> align_sc(Iterator begin, Iterator end,
int gap, score_matrix const & matrix,
double score_part)
{
struct results_vector
{
std::vector<alignment_result> m_vec;
double m_score;
results_vector(double s) : m_score(s)
{
}
bool operator()(alignment_result && res)
{
if (res.score >= m_score)
{
m_vec.push_back(res);
}
return true;
}
};
std::string query(begin, end);
results_vector rv(score_part *
needleman_wunsch(query, query, gap,
matrix).back().back());
align_template(begin, end, gap, matrix, rv);
return rv.m_vec;
}
int map_consistence ( int NX, int NY, Map * combined_map, Map *map1, Map *map2,
double *total_ptr, double *gap_score) {
int i,j;
double val1, val2;
double total = 0;
double aln_score;
if (!NX) NX = map1->x2y_size; /* TODO: rename */
if (!NY) NY = map1->y2x_size; /* TODO: rename */
for (i=0; i<NX; i++) {
for (j=0; j<NY; j++) {
val1 = map1->sse_pair_score[i][j];
val2 = map2->sse_pair_score[i][j];
if ( val1 > val2) {
combined_map->sse_pair_score[i][j] = val1;
combined_map->cosine[i][j] = map1->cosine[i][j];
} else {
combined_map->sse_pair_score[i][j] = val2;
combined_map->cosine[i][j] = map2->cosine[i][j];
}
}
}
/* Needleman on combined sse_pair_score */
needleman_wunsch (NX, NY, combined_map->sse_pair_score,
combined_map->x2y, combined_map->y2x, &aln_score );
/* how do lengths compare? */
combined_map->matches = match_length (NX, combined_map->x2y);
if ( ! combined_map->matches ) {
combined_map->assigned_score = 0.0;
} else {
for (i=0; i<NX; i++) {
j = combined_map->x2y[i];
if (j<0) continue;
total += combined_map->sse_pair_score[i][j];
}
combined_map->assigned_score = total;
}
/* pass NULL for total_ptr if I don't need it */
if (total_ptr) *total_ptr = combined_map->assigned_score;
return 0;
}