def gaff(f, score=ra.BLOSUM62, gap_init= -11, gap_ext= -1, debug=False):
'''Main driver to solve the GAFF problem.'''
x, y = ro.fafsa_values(f)
d, (xx, yy) = ra.optimal_alignment(x, y, score, gap_init, gap_ext, debug=debug)
print d
print xx
print yy
def sims(f, debug=False, align="fit"):
"""Main driver to solve the SIMS problem."""
(s, t), score, gap_score = ro.fafsa_values(f), ra.FixedCost(1, -1), -1
d, (ss, tt) = ra.optimal_alignment(s, t, score, gap_score, gap_score, align=align, debug=debug)
print d
print ss
print tt
def gcon(f, debug=False):
'''Main driver to solve the GCON problem.'''
x, y = ro.fafsa_values(f)
d, (xx, yy) = ra.optimal_alignment(x, y, ra.BLOSUM62, -5, 0, debug=debug)
print d
print xx
print yy
return d
def loca(f, debug=False):
'''Main driver to solve the LOCA problem.'''
x, y = ro.fafsa_values(f)
d, (xx, yy) = ra.optimal_alignment(x, y, ra.PAM250, -5, -5, align='local', debug=debug, gap_symbol='')
return ro.join_list((d, xx, yy), delimiter='\n')
