def rec_align(g1, g2, seed, sims, seqsims, ec_mode, ed, m, sb, sb2, delta, alpha, seednum, outputdir, alignstop, timestop=None, debug=False):
if alignstop == -1:
alignstop = float('inf')
else:
alignstop = int(alignstop)
curralign = Alignment(seed, m, ec_mode, ed, sb, sb2, alpha, delta, seednum, outputdir, timestop, alignstop)
curralign.logfile = g1.name + "_" + g2.name + "_" + str(seednum) + ".log"
curralign.statsfile = g1.name + "_" + g2.name + "_" + str(seednum) + ".stats"
if debug:
print("seed: ", seed)
print("ec_mode: ", ec_mode)
print("ed: ", ed)
print("m: ", m)
print("sb: ", sb)
print("sb2: ", sb2)
print("delta: ", delta)
print("alpha: ", alpha)
print("seednum: ", seednum)
print("outputdir: ", outputdir)
print("timestop: ", timestop)
print("debug: ", debug)
candidatePairs = set()
if debug:
print("aligning inital seeds*************************************************************************")
print("graph 1:")
for i in range(len(g1)):
print(i,":",g1.get_neighbors(i))
print("graph 2:")
for i in range(len(g2)):
print(i,":",g2.get_neighbors(i))
for seed1, seed2 in seed:
if debug:
print((seed1,seed2))
curralign.g1seedstr += str(g1.nodes[seed1]) + " "
curralign.g2seedstr += str(g2.nodes[seed2]) + " "
curralign.aligned_pairs.add((seed1, seed2))
curralign.g1alignednodes.add(seed1)
curralign.g2alignednodes.add(seed2)
candidatePairs.update(get_new_neighbor_pairs(g1,g2,seed1,seed2,curralign.g1alignednodes, curralign.g2alignednodes, curralign.sb, curralign.sb2, sims, seqsims))
curralign.g1seedstr += curralign.g2seedstr
curralign.k = len(curralign.aligned_pairs)
print('initial alignment:',curralign.aligned_pairs)
if(debug):
print("ec1: " + str(curralign.ec1))
print("ec2: " + str(curralign.ec2))
aligncombs = structs.alignCombinations()
rec_alignhelper(g1, g2, curralign, candidatePairs, aligncombs, sims, seqsims,debug)
def rec_align(g1,
g2,
seed,
ec_mode,
ed,
m,
delta,
alpha,
seednum,
outputdir,
timestop=None,
debug=False):
curralign = Alignment(seed, m, ec_mode, ed, alpha, delta, seednum,
outputdir, timestop)
curralign.logfile = g1.name + "_" + g2.name + "_" + str(seednum) + ".log"
candidatePairs = set()
if debug:
print(
"aligning inital seeds*************************************************************************"
)
print("graph 1:")
for i in range(len(g1)):
print(i, ":", g1.get_neighbors(i))
print("graph 2:")
for i in range(len(g2)):
print(i, ":", g2.get_neighbors(i))
for seed1, seed2 in seed:
if debug:
print((seed1, seed2))
curralign.g1seedstr += str(g1.nodes[seed1]) + " "
curralign.g2seedstr += str(g2.nodes[seed2]) + " "
curralign.aligned_pairs.add((seed1, seed2))
curralign.g1alignednodes.add(seed1)
curralign.g2alignednodes.add(seed2)
candidatePairs.update(
get_new_neighbor_pairs(g1, g2, seed1, seed2,
curralign.g1alignednodes,
curralign.g2alignednodes))
curralign.g1seedstr += curralign.g2seedstr
curralign.k = len(curralign.aligned_pairs)
print('initial alignment:', curralign.aligned_pairs)
if (debug):
print("ec1: " + str(curralign.ec1))
print("ec2: " + str(curralign.ec2))
aligncombs = structs.alignCombinations()
rec_alignhelper(g1, g2, curralign, candidatePairs, aligncombs, debug)