def __init__(self, *args, **kwargs):
# These are needed (and the normal way to override from a python class)
Sofa.Core.Controller.__init__(self, *args, **kwargs)
self.init_done = False
self.mesh = None
edges = []
if kwargs["mesh"]:
self.mesh = kwargs["mesh"]
for edge in self.mesh.edges.value:
edges += [(edge[0], edge[1], 1)]
skel_graph = Graph()
for edge in edges:
skel_graph.add_edge(*edge)
self.startNode = kwargs["startNode"]
self.goalNode = kwargs["goalNode"]
self.path = dijkstra(skel_graph, self.startNode, self.goalNode)
print("shortest path from {} to {} is {}".format(
self.startNode, self.goalNode, self.path))
self.skelMO = None
if kwargs["skelMO"]:
self.skelMO = kwargs["skelMO"]
self.goalMO = None
if kwargs["goalMO"]:
self.goalMO = kwargs["goalMO"]
self.it = 0
self.max_it = 1000
def create_graph(list_of_seq):
"""Creates an overlap graph based on a list of sequences."""
super_string_graph = Graph()
num_seq = len(list_of_seq)
i = 0
while i < num_seq:
first = list_of_seq[i]
j = 0
while j < num_seq:
if i != j:
second = list_of_seq[j]
max_overlap = min(
len(first),
len(second)) # Maximum overlength is shortest sequence
min_overlap = max(
len(first), len(second)
) // 2 # Minimum overlap is half of the largest sequence
overlap = max_overlap
found = False
while overlap >= min_overlap and not found:
if suffix(first, overlap) == prefix(second, overlap):
super_string_graph.add_edge(first,
second,
weight=overlap)
found = True
overlap -= 1
j += 1
i += 1
return super_string_graph
