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# Copyright 2002 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2018 by Maximilian Greil. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""get/set abstraction for graph representation."""
from functools import reduce
class Graph:
"""A directed graph abstraction with labeled edges."""
def __init__(self, nodes=()):
"""Initialize a new Graph object."""
self._adjacency_list = {} # maps parent -> set of child objects
for n in nodes:
self._adjacency_list[n] = set()
self._label_map = {} # maps label -> set of (parent, child) pairs
self._edge_map = {} # maps (parent, child) pair -> label
def __eq__(self, g):
"""Return 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 __repr__(self):
"""Return a unique string representation of this graph."""
s = "<Graph: "
for key in sorted(self._adjacency_list):
values = sorted(
(x, self._edge_map[(key, x)]) for x in list(self._adjacency_list[key])
)
s += f"({key!r}: {','.join(repr(v) for v in values)})"
return s + ">"
def __str__(self):
"""Return a concise string description of this graph."""
nodenum = len(self._adjacency_list)
edgenum = reduce(
lambda x, y: x + y, [len(v) for v in self._adjacency_list.values()]
)
labelnum = len(self._label_map)
return (
"<Graph: "
+ str(nodenum)
+ " node(s), "
+ str(edgenum)
+ " edge(s), "
+ str(labelnum)
+ " unique label(s)>"
)
def add_node(self, node):
"""Add a node to this graph."""
if node not in self._adjacency_list:
self._adjacency_list[node] = set()
def add_edge(self, source, to, label=None):
"""Add an edge to this graph."""
if source not in self._adjacency_list:
raise ValueError("Unknown <from> node: " + str(source))
if to not in self._adjacency_list:
raise ValueError("Unknown <to> node: " + str(to))
if (source, to) in self._edge_map:
raise ValueError(str(source) + " -> " + str(to) + " exists")
self._adjacency_list[source].add(to)
if label not in self._label_map:
self._label_map[label] = set()
self._label_map[label].add((source, to))
self._edge_map[(source, to)] = label
def child_edges(self, parent):
"""Return a list of (child, label) pairs for parent."""
if parent not in self._adjacency_list:
raise ValueError("Unknown <parent> node: " + str(parent))
return [
(x, self._edge_map[(parent, x)])
for x in sorted(self._adjacency_list[parent])
]
def children(self, parent):
"""Return a list of unique children for parent."""
return sorted(self._adjacency_list[parent])
def edges(self, label):
"""Return a list of all the edges with this label."""
if label not in self._label_map:
raise ValueError("Unknown label: " + str(label))
return sorted(self._label_map[label])
def labels(self):
"""Return a list of all the edge labels in this graph."""
return sorted(self._label_map.keys())
def nodes(self):
"""Return a list of the nodes in this graph."""
return list(self._adjacency_list.keys())
def parent_edges(self, child):
"""Return a list of (parent, label) pairs for child."""
if child not in self._adjacency_list:
raise ValueError("Unknown <child> node: " + str(child))
parents = []
for parent, children in self._adjacency_list.items():
for x in children:
if x == child:
parents.append((parent, self._edge_map[(parent, child)]))
return sorted(parents)
def parents(self, child):
"""Return a list of unique parents for child."""
return sorted({x[0] for x in self.parent_edges(child)})
def remove_node(self, node):
"""Remove node and all edges connected to it."""
if node not in self._adjacency_list:
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] = {x for x in self._adjacency_list[n] if x != node}
# remove all referring pairs in label map
for label in list(self._label_map.keys()): # we're editing this!
lm = {
x for x in self._label_map[label] if (x[0] != node) and (x[1] != node)
}
# remove the entry completely if the label is now unused
if lm:
self._label_map[label] = lm
else:
del self._label_map[label]
# remove all referring entries in edge map
for edge in list(self._edge_map.keys()): # we're editing this!
if edge[0] == node or edge[1] == node:
del self._edge_map[edge]
def remove_edge(self, parent, child, label):
"""Remove 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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