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MultiGraph.py

# Copyright 2001 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 *

00009 class MultiGraph:
    """A directed multigraph abstraction with labeled edges."""

00012     def __init__(self, nodes = []):
        """Initializes a new MultiGraph object."""
        self.__adjacency_list = {}    # maps parent -> set of (child, label) pairs
        for n in nodes:
            self.__adjacency_list[n] = HashSet()
        self.__label_map = {}         # maps label -> set of (parent, child) pairs

00019     def __eq__(self, g):
        """Returns true if g is equal to this graph."""
        return isinstance(g, MultiGraph) and \
               (self.__adjacency_list == g.__adjacency_list) and \
               (self.__label_map == g.__label_map)

00025     def __ne__(self, g):
        """Returns true if g is not equal to this graph."""
        return not self.__eq__(g)

00029     def __repr__(self):
        """Returns an unique string representation of this graph."""
        s = "<MultiGraph: "
        keys = self.__adjacency_list.keys()
        keys.sort()
        for key in keys:
            values = self.__adjacency_list[key].list()
            values.sort()
            s = s + "(" + repr(key) + ": " + ",".join(map(repr, values)) + ")" 
        return s + ">"

00040     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 "<MultiGraph: " + \
               str(nodenum) + " node(s), " + \
               str(edgenum) + " edge(s), " + \
               str(labelnum) + " unique label(s)>"

00051     def add_node(self, node):
        """Adds a node to this graph."""
        if not self.__adjacency_list.has_key(node):
            self.__adjacency_list[node] = HashSet()

00056     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)
        edge = (to, label)
        self.__adjacency_list[source].add(edge)
        if not self.__label_map.has_key(label):
            self.__label_map[label] = HashSet()
        self.__label_map[label].add((source,to))

00068     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 self.__adjacency_list[parent].list()

00074     def children(self, parent):
        """Returns a list of unique children for parent."""
        s = HashSet([x[0] for x in self.child_edges(parent)])
        return s.list()

00079     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()

00085     def labels(self):
        """Returns a list of all the edge labels in this graph."""
        return self.__label_map.keys()

00089     def nodes(self):
        """Returns a list of the nodes in this graph."""
        return self.__adjacency_list.keys()

00093     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[0] is child:
                    parents.append((parent, x[1]))
        return parents

00105     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()

00110     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[0] 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

00131     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"

# auxilliary graph functions

def df_search(graph, root = None):
    """Depth first search of g.

    Returns a list of all nodes that can be reached from the root node
    in depth-first order.

    If root is not given, the search will be rooted at an arbitrary node.
    """
    seen = {}
    search = []
    if len(g.nodes()) < 1:
        return search
    if root is None:
        root = (g.nodes())[0]
    seen[root] = 1
    search.append(root)
    current = g.children(root)
    while len(current) > 0:
        node = current[0]
        current = current[1:]
        if not seen.has_key(node):
            search.append(node)
            seen[node] = 1
            current = g.children(node) + current
    return search   

def bf_search(graph, root = None):
    """Breadth first search of g.

    Returns a list of all nodes that can be reached from the root node
    in breadth-first order.

    If root is not given, the search will be rooted at an arbitrary node.
    """
    seen = {}
    search = []
    if len(g.nodes()) < 1:
        return search
    if root is None:
        root = (g.nodes())[0]
    seen[root] = 1
    search.append(root)
    current = g.children(root)
    while len(current) > 0:
        node = current[0]
        current = current[1:]
        if not seen.has_key(node):
            search.append(node)
            seen[node] = 1
            current.extend(g.children(node))
    return search




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