Function naive_aamp_match

tests/test_aamp_motifs.py:22–43

(Q, T, p, excl_zone, max_distance)

def naive_aamp_match(Q, T, p, excl_zone, max_distance):
    m = Q.shape[0]
    D = naive.aamp_distance_profile(Q, T, m, p)

    # Finds all indices that have a lower distance profile value `D`
    # than `atol + rtol * D`
    matches = []
    for i in range(D.size):
        dist = D[i]
        if dist <= max_distance:
            matches.append(i)

    # Removes indices that are inside the exclusion zone of some occurrence with
    # a smaller distance to the query
    matches.sort(key=lambda x: D[x])
    result = []
    while len(matches) > 0:
        o = matches[0]
        result.append([D[o], o])
        matches = [x for x in matches if x < o - excl_zone or x > o + excl_zone]

    return np.array(result, dtype=object)


def test_aamp_motifs_one_motif():