def generate_continuations(self, sym, ind, original_seq):
postfix_len = 4
seqs = []
seq_inds = []
for i in range(2, postfix_len):
fixed = {ind:sym}
fixed[ind+i] = 'I'
seq, inds = \
shortest_path(self.model, fixed, ind, original_seq)
seqs.append(seq)
seq_inds.append(inds)
return seqs, seq_inds
def generate_ripples(self, original_seq, sym_ind, sims, win_max=2):
print '...generate_ripples', sims
seq_subs = []
seq_inds = []
for win in range(1, win_max):
ub = sym_ind + win
lb = sym_ind - win
# allow one extra seq step
lb_out_bound = lb < -1
ub_out_bound = ub > len(original_seq)
# supposedly already second time out of bound
if lb_out_bound or ub_out_bound:
break
if lb < 0:
lb = 0
if ub > len(original_seq):
ub = len(original_seq)
for j, s in enumerate(sims):
fixed = {}
if ub < len(original_seq):
fixed[ub] = original_seq[ub]
else:
fixed[ub] = []
fixed[lb] = original_seq[lb]
# may override lb or ub
fixed[sym_ind] = s
print fixed
sub_seq, sym_inds = \
shortest_path(self.model, fixed, sym_ind, original_seq)
seq_subs.append(sub_seq)
seq_inds.append(list(sym_inds))
for seq in seq_subs:
print seq
return seq_subs, seq_inds
