def test_repr(self):
st = SuffixTree("t")
output = '\tStart \tEnd \tSuf \tFirst \tLast \tString\n\t0 \t1 \t-1 \t0 \t0 \tt\n'
import pdb
pdb.set_trace()
self.assertEqual(st.__repr__(), output)
def test_repr(self):
st = SuffixTree("t")
output = '\tStart \tEnd \tSuf \tFirst \tLast \tString\n\t0 \t1 \t-1 \t0 \t0 \tt\n'
import pdb;pdb.set_trace()
self.assertEqual(st.__repr__(), output)
def test_repr(self):
st = SuffixTree("t")
output = '\tStart \tEnd \tSuf \tFirst \tLast \tString\n\t0 \t1 \t-1 \t0 \t0 \t\nt\n'
self.assertEqual(st.__repr__(), output)
class SuffixClassifier(object):
def __init__(self, D_plus, D_minus, alphabet):
self.word = '1'.join(D_plus) + '1' + '0'.join(D_minus) + '0$'
self.suffixTree = SuffixTree(self.word)
self.alphabet = alphabet | {'0', '1', '$'}
self.edges = self.suffixTree.edges
if self.__has_edges(0): # bug fix
self.suffixTree.nodes[0].suffix_node = 0
def print_suffix_tree(self, printDirectDebug = True):
print(self.word)
self.print_tree_part('0', 0)
print()
if printDirectDebug:
print(self.suffixTree.__repr__())
def print_tree_part(self, prefix, nodeId):
found = False
first = True
for e in self.suffixTree.edges.values():
if e.source_node_index == nodeId:
found = True
text = self.suffixTree.string[e.first_char_index:e.last_char_index+1]
if first:
first = False
else:
prefix = (' ' * (len(prefix) - 1)) + '\\'
data_node = self.__print_data_node(e.source_node_index)
link = "%s%s--'%s'--%d" % (prefix, data_node, text, e.dest_node_index)
if not self.__has_edges(e.dest_node_index):
link += self.__print_data_node(e.dest_node_index)
self.print_tree_part(link, e.dest_node_index)
if found == False:
print(('\n' if prefix[0] in ['0','\\'] else '') + prefix)
def __print_data_node(self, nodeId):
if hasattr(self.suffixTree.nodes[nodeId], 'negative'):
node = self.suffixTree.nodes[nodeId]
return "(%d,%d)" % (node.negative, node.positive)
return ""
def truncate_tree(self):
self.nodes = {} # convert to dictionary because we need node
# at specific index after remove any elements before
for i in range(len(self.suffixTree.nodes)):
u = self.suffixTree.nodes[i]
u.positive = 0 #n_+
u.negative = 0 #n_-
self.nodes[i] = u
self.__truncate(0)
def __truncate(self, u: int):
for v, l in self.__traverse(u):
if not any(c in l for c in ['0','1','$']): # case (a)
self.__truncate(v)
elif l[0] in ['0', '1']: # (b) or (c)
leafs = self.__remove_with_edge(u, v, l)
self.__increment(u, l[0], leafs)
elif l[0] == '$': #(d)
self.edges.pop((u, l[0]))
self.nodes.pop(v) # not remove u!
else:
e = self.edges[(u, l[0])]
sub = e.first_char_index
for c in l:
if c in ['0', '1']: # (e) or (f)
leafs = self.__remove_from_node(v)
self.__increment(v, c, leafs)
break
sub += 1
e.last_char_index = sub - 1
def __remove_from_node(self, u: int): #remove subtree from node
if self.nodes[u].suffix_node == -1: #speedup, leaf
return 1
leafs = 0
for v, l in self.__traverse(u):
leafs += self.__remove_from_node(v)
self.edges.pop((u, l[0]))
self.nodes.pop(v)
self.nodes[u].suffix_node = -1
return leafs
def __remove_with_edge(self, u: int, v: int, l: Label): #remove subtree from edge
leafs = self.__remove_from_node(v)
self.edges.pop((u, l[0]))
self.nodes.pop(v)
#check if u is not leaf now
if not self.__has_edges(u):
self.nodes[u].suffix_node = -1
return leafs
def recalculate(self, u):
if self.nodes[u].suffix_node == -1:
return self.nodes[u].negative, self.nodes[u].positive
negative = 0
positive = 0
for v, l in self.__traverse(u):
neg, pos = self.recalculate(v)
negative += neg
positive += pos
self.__increment(u, '0', negative)
self.__increment(u, '1', positive)
return self.nodes[u].negative, self.nodes[u].positive
def __increment(self, u: int, type: str, leafs):
if type == '0':
self.nodes[u].negative += leafs
else:
self.nodes[u].positive += leafs
def __has_edges(self, u: int):
return any(self.__traverse(u))
def __traverse(self, u):
for c in self.alphabet:
if (u, c) in self.edges:
e = self.edges[(u, c)]
l = Label(self, e.first_char_index, e.last_char_index)
yield (e.dest_node_index, l)
class SuffixClassifier(object):
def __init__(self, D_plus, D_minus, alphabet):
self.word = '1'.join(D_plus) + '1' + '0'.join(D_minus) + '0$'
self.suffixTree = SuffixTree(self.word)
self.alphabet = alphabet | {'0', '1', '$'}
self.edges = self.suffixTree.edges
if self.__has_edges(0): # bug fix
self.suffixTree.nodes[0].suffix_node = 0
def print_suffix_tree(self, printDirectDebug=True):
print(self.word)
self.print_tree_part('0', 0)
print()
if printDirectDebug:
print(self.suffixTree.__repr__())
def print_tree_part(self, prefix, nodeId):
found = False
first = True
for e in self.suffixTree.edges.values():
if e.source_node_index == nodeId:
found = True
text = self.suffixTree.string[e.first_char_index:e.
last_char_index + 1]
if first:
first = False
else:
prefix = (' ' * (len(prefix) - 1)) + '\\'
data_node = self.__print_data_node(e.source_node_index)
link = "%s%s--'%s'--%d" % (prefix, data_node, text,
e.dest_node_index)
if not self.__has_edges(e.dest_node_index):
link += self.__print_data_node(e.dest_node_index)
self.print_tree_part(link, e.dest_node_index)
if found == False:
print(('\n' if prefix[0] in ['0', '\\'] else '') + prefix)
def __print_data_node(self, nodeId):
if hasattr(self.suffixTree.nodes[nodeId], 'negative'):
node = self.suffixTree.nodes[nodeId]
return "(%d,%d)" % (node.negative, node.positive)
return ""
def truncate_tree(self):
self.nodes = {} # convert to dictionary because we need node
# at specific index after remove any elements before
for i in range(len(self.suffixTree.nodes)):
u = self.suffixTree.nodes[i]
u.positive = 0 #n_+
u.negative = 0 #n_-
self.nodes[i] = u
self.__truncate(0)
def __truncate(self, u: int):
for v, l in self.__traverse(u):
if not any(c in l for c in ['0', '1', '$']): # case (a)
self.__truncate(v)
elif l[0] in ['0', '1']: # (b) or (c)
leafs = self.__remove_with_edge(u, v, l)
self.__increment(u, l[0], leafs)
elif l[0] == '$': #(d)
self.edges.pop((u, l[0]))
self.nodes.pop(v) # not remove u!
else:
e = self.edges[(u, l[0])]
sub = e.first_char_index
for c in l:
if c in ['0', '1']: # (e) or (f)
leafs = self.__remove_from_node(v)
self.__increment(v, c, leafs)
break
sub += 1
e.last_char_index = sub - 1
def __remove_from_node(self, u: int): #remove subtree from node
if self.nodes[u].suffix_node == -1: #speedup, leaf
return 1
leafs = 0
for v, l in self.__traverse(u):
leafs += self.__remove_from_node(v)
self.edges.pop((u, l[0]))
self.nodes.pop(v)
self.nodes[u].suffix_node = -1
return leafs
def __remove_with_edge(self, u: int, v: int,
l: Label): #remove subtree from edge
leafs = self.__remove_from_node(v)
self.edges.pop((u, l[0]))
self.nodes.pop(v)
#check if u is not leaf now
if not self.__has_edges(u):
self.nodes[u].suffix_node = -1
return leafs
def recalculate(self, u):
if self.nodes[u].suffix_node == -1:
return self.nodes[u].negative, self.nodes[u].positive
negative = 0
positive = 0
for v, l in self.__traverse(u):
neg, pos = self.recalculate(v)
negative += neg
positive += pos
self.__increment(u, '0', negative)
self.__increment(u, '1', positive)
return self.nodes[u].negative, self.nodes[u].positive
def __increment(self, u: int, type: str, leafs):
if type == '0':
self.nodes[u].negative += leafs
else:
self.nodes[u].positive += leafs
def __has_edges(self, u: int):
return any(self.__traverse(u))
def __traverse(self, u):
for c in self.alphabet:
if (u, c) in self.edges:
e = self.edges[(u, c)]
l = Label(self, e.first_char_index, e.last_char_index)
yield (e.dest_node_index, l)
