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# Copyright 2002 by Tarjei Mikkelsen. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# get set abstraction for graph representation
from Bio.Pathway.Rep.HashSet import *
class Graph:
"""A directed graph abstraction with labeled edges."""
def __init__(self, nodes = []):
"""Initializes a new Graph object."""
self.__adjacency_list = {} # maps parent -> set of child objects
for n in nodes:
self.__adjacency_list[n] = HashSet()
self.__label_map = {} # maps label -> set of (parent, child) pairs
self.__edge_map = {} # maps (parent, child) pair -> label
def __eq__(self, g):
"""Returns true if g is equal to this graph."""
return isinstance(g, Graph) and \
(self.__adjacency_list == g.__adjacency_list) and \
(self.__label_map == g.__label_map) and \
(self.__edge_map == g.__edge_map)
def __ne__(self, g):
"""Returns true if g is not equal to this graph."""
return not self.__eq__(g)
def __repr__(self):
"""Returns an unique string representation of this graph."""
s = "<Graph: "
keys = self.__adjacency_list.keys()
keys.sort()
for key in keys:
values = [(x,self.__edge_map[(key,x)]) \
for x in self.__adjacency_list[key].list()]
values.sort()
s = s + "(" + repr(key) + ": " + ",".join(map(repr, values)) + ")"
return s + ">"
def __str__(self):
"""Returns a concise string description of this graph."""
nodenum = len(self.__adjacency_list.keys())
edgenum = reduce(lambda x,y: x+y,
map(len, self.__adjacency_list.values()))
labelnum = len(self.__label_map.keys())
return "<Graph: " + \
str(nodenum) + " node(s), " + \
str(edgenum) + " edge(s), " + \
str(labelnum) + " unique label(s)>"
def add_node(self, node):
"""Adds a node to this graph."""
if not self.__adjacency_list.has_key(node):
self.__adjacency_list[node] = HashSet()
def add_edge(self, source, to, label = None):
"""Adds an edge to this graph."""
if not self.__adjacency_list.has_key(source):
raise ValueError, "Unknown <from> node: " + str(source)
if not self.__adjacency_list.has_key(to):
raise ValueError, "Unknown <to> node: " + str(to)
if self.__edge_map.has_key((source,to)):
raise ValueError, str(source) + " -> " + str(to) + " exists"
self.__adjacency_list[source].add(to)
if not self.__label_map.has_key(label):
self.__label_map[label] = HashSet()
self.__label_map[label].add((source,to))
self.__edge_map[(source,to)] = label
def child_edges(self, parent):
"""Returns a list of (child, label) pairs for parent."""
if not self.__adjacency_list.has_key(parent):
raise ValueError, "Unknown <parent> node: " + str(parent)
return [(x, self.__edge_map[(parent,x)]) \
for x in self.__adjacency_list[parent].list()]
def children(self, parent):
"""Returns a list of unique children for parent."""
return self.__adjacency_list[parent].list()
def edges(self, label):
"""Returns a list of all the edges with this label."""
if not self.__label_map.has_key(label):
raise ValueError, "Unknown label: " + str(label)
return self.__label_map[label].list()
def labels(self):
"""Returns a list of all the edge labels in this graph."""
return self.__label_map.keys()
def nodes(self):
"""Returns a list of the nodes in this graph."""
return self.__adjacency_list.keys()
def parent_edges(self, child):
"""Returns a list of (parent, label) pairs for child."""
if not self.__adjacency_list.has_key(child):
raise ValueError, "Unknown <child> node: " + str(child)
parents = []
for parent in self.__adjacency_list.keys():
children = self.__adjacency_list[parent]
for x in children.list():
if x is child:
parents.append((parent, self.__edge_map[(parent, child)]))
return parents
def parents(self, child):
"""Returns a list of unique parents for child."""
s = HashSet([x[0] for x in self.parent_edges(child)])
return s.list()
def remove_node(self, node):
"""Removes node and all edges connected to it."""
if not self.__adjacency_list.has_key(node):
raise ValueError, "Unknown node: " + str(node)
# remove node (and all out-edges) from adjacency list
del self.__adjacency_list[node]
# remove all in-edges from adjacency list
for n in self.__adjacency_list.keys():
self.__adjacency_list[n] = HashSet(filter(lambda x,node=node: x is not node,
self.__adjacency_list[n].list()))
# remove all refering pairs in label map
for label in self.__label_map.keys():
lm = HashSet(filter(lambda x,node=node: \
(x[0] is not node) and (x[1] is not node),
self.__label_map[label].list()))
# remove the entry completely if the label is now unused
if lm.empty():
del self.__label_map[label]
else:
self.__label_map[label] = lm
# remove all refering entries in edge map
for edge in self.__edge_map.keys():
if edge[0] is node or edge[1] is node:
del self.__edge_map[edge]
def remove_edge(self, parent, child, label):
"""Removes edge. -- NOT IMPLEMENTED"""
# hm , this is a multigraph - how should this be implemented?
raise NotImplementedError, "remove_edge is not yet implemented"
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