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utility::graph::Graph Class Reference

A Graph with constant time edge insertion and deletion. Extensible. More...

#include <Graph.hh>

Inheritance diagram for utility::graph::Graph:
Inheritance graph
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Public Types

typedef utility::vector1< Node * > NodeVector
 
typedef Node::EdgeListIter EdgeListIter
 
typedef Node::EdgeListConstIter EdgeListConstIter
 
typedef utility::VirtualBase parent
 

Public Member Functions

GraphCOP get_self_ptr () const
 self pointers More...
 
GraphOP get_self_ptr ()
 
 ~Graph () override
 virtual destructor. Derived classes must ensure they've destroyed all their nodes and edges through a call to "destroy_everything" before this function is arrived at More...
 
 Graph ()
 ctor More...
 
 Graph (platform::Size num_nodes)
 num nodes ctor More...
 
 Graph (Graph const &source)
 copy ctor. Must not be called by derived class copy ctors. More...
 
Graphoperator= (Graph const &source)
 assignment operator. source and this must have the same type. More...
 
void copy_connectivity (Graph const &source)
 copy the edge connectivity from a source graph with a potentially unknown type. More...
 
platform::Size num_nodes () const
 the number of nodes in the graph More...
 
void set_num_nodes (platform::Size num_nodes)
 set the number of nodes in the graph – deletes any existing edges in the graph More...
 
Edgeadd_edge (platform::Size node1, platform::Size node2)
 add an edge between two vertices. Invokes "create_edge" from the derived class. Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge. More...
 
Edgeadd_edge (Edge const *example_edge)
 add an edge to this graph copying the data from an edge in another graph. Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge. More...
 
bool get_edge_exists (platform::Size node1, platform::Size node2) const
 is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges More...
 
void drop_all_edges ()
 delete all the edges present in the graph More...
 
void drop_all_edges_for_node (platform::Size node)
 delete all the edges for a single vertex in the graph More...
 
void print_vertices () const
 send summary information to the screen for all vertices in the graph More...
 
void output_connectivity (std::ostream &os) const
 send an edge list to the stream os. More...
 
void output_dimacs (std::ostream &os) const
 describe this graph in dimacs form to the stream os. More...
 
ObjexxFCL::FArray2D_int all_pairs_shortest_paths () const
 O(V^3). Computes all pairs shortest paths using Warshall's algorithm and writes all the path distances to the two-dimensional table. More...
 
Node const * get_node (platform::Size index) const
 
Nodeget_node (platform::Size index)
 
platform::Size num_edges () const
 
EdgeListConstIter const_edge_list_begin () const
 returns a const iterator to the beginning of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...
 
EdgeListIter edge_list_begin ()
 returns a non-const iterator to the beginning of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...
 
EdgeListConstIter const_edge_list_end () const
 returns a const iterator to the end of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...
 
EdgeListIter edge_list_end ()
 returns a non-const iterator to the end of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...
 
Edgefind_edge (platform::Size node1, platform::Size node2)
 returns a pointer to the edge connecting nodes node1 and node2, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval. More...
 
Edge const * find_edge (platform::Size node1, platform::Size node2) const
 returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval. More...
 
Edgefocused_edge ()
 returns a pointer to the focused edge More...
 
Edge const * focused_edge () const
 returns a const-pointer to the focused edge More...
 
virtual void delete_edge (Edge *edge)
 remove an edge from the graph. (NEW AS OF 12/9/07) Never call C++'s "delete" function on an edge pointer directly. Derived classes must implement this function. If they wish to use unordered_object_pools to manage their memory More...
 
platform::Size getTotalMemoryUsage () const
 returns a count of all the memory used by every vertex and edge in a graph by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class. More...
 
- Public Member Functions inherited from utility::VirtualBase
 VirtualBase ()=default
 Default constructor. More...
 
virtual ~VirtualBase ()=default
 The virtual destructor is one of the main reasons for the VirtualBase class. More...
 
 VirtualBase (VirtualBase const &)=default
 
 VirtualBase (VirtualBase &&)=default
 
VirtualBaseoperator= (VirtualBase const &)=default
 
VirtualBaseoperator= (VirtualBase &&)=default
 

Protected Member Functions

virtual platform::Size count_static_memory () const
 
virtual platform::Size count_dynamic_memory () const
 
void drop_edge (EdgeListIter edge_iter)
 remove an edge from the entire-graph edge list. Called only by class Edge during its destructor More...
 
void delete_everything ()
 deallocate all nodes and edges from the graph More...
 
virtual void delete_node (Node *)
 Only called by delete_everything(). Does not need to be overriden unless derived class generates nodes in a fancy way. More...
 
virtual Nodecreate_new_node (platform::Size node_index)
 factory method for node creation, defined by derived graph classes, called by the base class More...
 
virtual Edgecreate_new_edge (platform::Size index1, platform::Size index2)
 factory method for edge creation, defined by derived graph classes, called by the base class More...
 
virtual Edgecreate_new_edge (Edge const *example_edge)
 factory method for edge copy-construction. Derived class should downcast the example_edge pointer and may read that edge's data. More...
 
boost::unordered_object_pool
< EdgeListElement > & 
edge_list_element_pool ()
 Used by class Node only, this is the pool from which edge lists are to allocate their edge lists elements from. More...
 

Private Attributes

platform::Size num_nodes_
 
NodeVector nodes_
 
platform::Size num_edges_
 
boost::unordered_object_pool
< EdgeListElement > * 
edge_list_element_pool_
 the pool from which edge lists are to allocate their edge list elements More...
 
EdgeList edge_list_
 
boost::unordered_object_pool
< Edge > * 
edge_pool_
 the pool from which class Graph allocates Edge objects. Not used by derived classes More...
 
Edgefocused_edge_
 Quick-access to a frequently needed edge – the most recently sought edge in a call to find_edge() or the most recently added edge. More...
 

Friends

class Node
 
class Edge
 

Detailed Description

A Graph with constant time edge insertion and deletion. Extensible.

Member Typedef Documentation

Constructor & Destructor Documentation

utility::graph::Graph::~Graph ( )
override

virtual destructor. Derived classes must ensure they've destroyed all their nodes and edges through a call to "destroy_everything" before this function is arrived at

destructor

References delete_everything(), edge_list_element_pool_, and edge_pool_.

utility::graph::Graph::Graph ( )

ctor

default constructor; creates an empty graph (no nodes, no edges)

Referenced by count_static_memory().

utility::graph::Graph::Graph ( platform::Size  num_nodes)

num nodes ctor

Danger! Danger! The C++ standard prevents function overrides from being called from a base class constructor. If you use this constructor without subsequently calling set_num_nodes(), you'll end up with a graph populated with utility::graph::Node nodes instead of derived nodes.

Do not call this constructor from a derived class in the initialization list, since this constructor calls the polymorphic function create_new_node, and polymorphism does not work during constructors or destructors.

Parameters
num_ig_nodes- [in] - number of nodes that this graph will contain

References create_new_node(), test.T200_Scoring::ii, nodes_, and num_nodes().

utility::graph::Graph::Graph ( Graph const &  source)

copy ctor. Must not be called by derived class copy ctors.

copy constructor relies on factory methods and virtual "copy_from" methods

This copy constructor should NOT be used by derived classes. At the time this is called, the identity of this has not yet been resolved – this constructor will produce Node and Edge objects when it calls "create_new_node" and not DerivedNode or DerivedEdge objects. Derived class copy constructors should call the base class assignment operator once the initial construction has been completed.

References add_edge(), const_edge_list_begin(), const_edge_list_end(), utility::graph::Edge::copy_from(), create_new_node(), find_edge(), test.T200_Scoring::ii, nodes_, and num_nodes_.

Member Function Documentation

Edge * utility::graph::Graph::add_edge ( platform::Size  index1,
platform::Size  index2 
)

add an edge between two vertices. Invokes "create_edge" from the derived class. Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order. For speed, does NOT check to see if edge already exists – except in debug mode.

uses factory method create_new_edge and adds the created edge to the graph's edge list. Not threadsafe. Only a single thread should add edges to the graph at a time.

Parameters
index1- [in] - index of one of the two nodes the edge is to connect
index2- [in] - index of the second of the two nodes the edge is to connect

References create_new_edge(), debug_assert, edge_list_, focused_edge_, get_edge_exists(), utility::graph::EdgeList::last(), num_edges_, utility::graph::EdgeList::push_back(), utility::graph::Edge::set_pos_in_owners_list(), and erraser_analysis::temp.

Referenced by copy_connectivity(), Graph(), and operator=().

Edge * utility::graph::Graph::add_edge ( Edge const *  example_edge)

add an edge to this graph copying the data from an edge in another graph. Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

for use in Graph operator=

Uses the edge copy constructor so that data stored on edges of one graph may be placed rapidly into the new edge of this graph.

References utility::graph::EdgeList::begin(), create_new_edge(), debug_assert, edge_list_, focused_edge_, get_edge_exists(), utility::graph::Edge::get_first_node_ind(), utility::graph::Edge::get_second_node_ind(), num_edges_, utility::graph::EdgeList::push_front(), and utility::graph::Edge::set_pos_in_owners_list().

FArray2D_int utility::graph::Graph::all_pairs_shortest_paths ( ) const

O(V^3). Computes all pairs shortest paths using Warshall's algorithm and writes all the path distances to the two-dimensional table.

compute all node distances and return FArray2D with that information

O(n^3)

References debug_assert, edge_list_, test.T200_Scoring::ii, and num_nodes_.

EdgeListConstIter utility::graph::Graph::const_edge_list_begin ( ) const
inline

returns a const iterator to the beginning of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex

References utility::graph::EdgeList::const_begin(), and edge_list_.

Referenced by copy_connectivity(), Graph(), and operator=().

EdgeListConstIter utility::graph::Graph::const_edge_list_end ( ) const
inline

returns a const iterator to the end of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex

References utility::graph::EdgeList::const_end(), and edge_list_.

Referenced by copy_connectivity(), Graph(), and operator=().

void utility::graph::Graph::copy_connectivity ( Graph const &  source)

copy the edge connectivity from a source graph with a potentially unknown type.

copy the connectivity of the source graph, but do not copy the data stored in the nodes and edges of the source graph. Useful for when copying a graph of a different type (e.g. from an EnergyGraph into a Graph)

References add_edge(), const_edge_list_begin(), const_edge_list_end(), drop_all_edges(), num_nodes_, and set_num_nodes().

platform::Size utility::graph::Graph::count_dynamic_memory ( ) const
protectedvirtual

References num_edges_, and num_nodes_.

Referenced by getTotalMemoryUsage().

platform::Size utility::graph::Graph::count_static_memory ( ) const
protectedvirtual

References Graph().

Referenced by getTotalMemoryUsage().

Edge * utility::graph::Graph::create_new_edge ( platform::Size  index1,
platform::Size  index2 
)
protectedvirtual

factory method for edge creation, defined by derived graph classes, called by the base class

factory method for edge creation Should be overriden in derived classes

References edge_pool_.

Referenced by add_edge().

Edge * utility::graph::Graph::create_new_edge ( Edge const *  example_edge)
protectedvirtual

factory method for edge copy-construction. Derived class should downcast the example_edge pointer and may read that edge's data.

References edge_pool_, utility::graph::Edge::get_first_node_ind(), and utility::graph::Edge::get_second_node_ind().

Node * utility::graph::Graph::create_new_node ( platform::Size  node_index)
protectedvirtual

factory method for node creation, defined by derived graph classes, called by the base class

factory method for node creation Should be overriden in derived classes

References Node.

Referenced by Graph(), and set_num_nodes().

void utility::graph::Graph::delete_edge ( Edge edge)
virtual

remove an edge from the graph. (NEW AS OF 12/9/07) Never call C++'s "delete" function on an edge pointer directly. Derived classes must implement this function. If they wish to use unordered_object_pools to manage their memory

References edge_pool_.

Referenced by utility::graph::delete_all_intragroup_edges(), delete_everything(), utility::graph::Node::drop_all_edges(), and drop_all_edges().

void utility::graph::Graph::delete_everything ( )
protected

deallocate all nodes and edges from the graph

deletes each edge in the graph and then deletes each node

its important to note that nodes must outlive their incident edges

References utility::graph::EdgeList::begin(), delete_edge(), delete_node(), edge_list_, utility::graph::EdgeList::end(), focused_edge_, test.T200_Scoring::ii, nodes_, and num_nodes_.

Referenced by set_num_nodes(), and ~Graph().

void utility::graph::Graph::delete_node ( Node node)
protectedvirtual

Only called by delete_everything(). Does not need to be overriden unless derived class generates nodes in a fancy way.

Referenced by delete_everything().

void utility::graph::Graph::drop_all_edges ( )

delete all the edges present in the graph

deletes all edges in the graph

References utility::graph::EdgeList::begin(), delete_edge(), edge_list_, and utility::graph::EdgeList::end().

Referenced by copy_connectivity(), and operator=().

void utility::graph::Graph::drop_all_edges_for_node ( platform::Size  node)

delete all the edges for a single vertex in the graph

deletes all edges adjacent to the node specified

Parameters
node- [in] - index of the node

References utility::graph::Node::drop_all_edges(), and get_node().

void utility::graph::Graph::drop_edge ( EdgeListIter  iter)
protected

remove an edge from the entire-graph edge list. Called only by class Edge during its destructor

removes edge from edge list at iterator iter

each edge keeps track of its position in its owner's graph's edge list so it can efficiently delete itself should it need to.

Parameters
iter- [in] - the iterator in the non-const edge list pointing at the edge that's deleting itself
citer- [in] - the iterator in the const edge list pointing at the edge that's deleting itself

References edge_list_, utility::graph::EdgeList::erase(), focused_edge_, and num_edges_.

Referenced by utility::graph::Edge::~Edge().

EdgeListIter utility::graph::Graph::edge_list_begin ( )
inline

returns a non-const iterator to the beginning of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex

References utility::graph::EdgeList::begin(), and edge_list_.

Referenced by utility::graph::delete_all_intragroup_edges().

boost::unordered_object_pool< EdgeListElement >& utility::graph::Graph::edge_list_element_pool ( )
inlineprotected

Used by class Node only, this is the pool from which edge lists are to allocate their edge lists elements from.

References edge_list_element_pool_.

EdgeListIter utility::graph::Graph::edge_list_end ( )
inline

returns a non-const iterator to the end of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex

References edge_list_, and utility::graph::EdgeList::end().

Referenced by utility::graph::delete_all_intragroup_edges().

Edge * utility::graph::Graph::find_edge ( platform::Size  node1,
platform::Size  node2 
)

returns a pointer to the edge connecting nodes node1 and node2, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

returns the edge connecting node1 and node2

graph keeps a pointer to the last edge that was accessed to that search is fairly efficient.

Parameters
node1- [in] - index of the first node
node2- [in] - index of the second node

References focused_edge_, nodes_, and utility::graph::Edge::same_edge().

Referenced by get_edge_exists(), and Graph().

Edge const * utility::graph::Graph::find_edge ( platform::Size  node1,
platform::Size  node2 
) const

returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

returns the edge connecting node1 and node2 (const version)

graph keeps a pointer to the last edge that was accessed to that search is fairly efficient.

Parameters
node1- [in] - index of the first node
node2- [in] - index of the second node

References focused_edge_, nodes_, and utility::graph::Edge::same_edge().

Edge* utility::graph::Graph::focused_edge ( )
inline

returns a pointer to the focused edge

References focused_edge_.

Edge const* utility::graph::Graph::focused_edge ( ) const
inline

returns a const-pointer to the focused edge

References focused_edge_.

bool utility::graph::Graph::get_edge_exists ( platform::Size  node1,
platform::Size  node2 
) const

is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges

returns true if an edge between node1 and node2 exists

Parameters
node1- [in] - index of the one of the nodes
node2- [in] - index of the other node

References find_edge().

Referenced by add_edge().

Node const* utility::graph::Graph::get_node ( platform::Size  index) const
inline
Node* utility::graph::Graph::get_node ( platform::Size  index)
inline
GraphCOP utility::graph::Graph::get_self_ptr ( ) const
inline

self pointers

GraphOP utility::graph::Graph::get_self_ptr ( )
inline
platform::Size utility::graph::Graph::getTotalMemoryUsage ( ) const

returns a count of all the memory used by every vertex and edge in a graph by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class.

References utility::graph::EdgeList::const_begin(), utility::graph::EdgeList::const_end(), count_dynamic_memory(), count_static_memory(), edge_list_, test.T200_Scoring::ii, nodes_, and num_nodes().

platform::Size utility::graph::Graph::num_edges ( ) const
inline

References num_edges_.

Referenced by output_dimacs().

platform::Size utility::graph::Graph::num_nodes ( ) const
inline
Graph & utility::graph::Graph::operator= ( Graph const &  source)

assignment operator. source and this must have the same type.

operator = (). Relies on factory methods and virtual "copy_from" methods

operator= must only be performed on graphs of the same type e.g. an EnergyGraph may be copied from another EnergyGraph, but should not be copied from a Graph.

References add_edge(), const_edge_list_begin(), const_edge_list_end(), drop_all_edges(), test.T200_Scoring::ii, nodes_, num_nodes_, and set_num_nodes().

void utility::graph::Graph::output_connectivity ( std::ostream &  os) const

send an edge list to the stream os.

writes out a list of all the edges in the graph

Parameters
os- [in] - the output stream to write to

References demo.D060_Folding::counter, and edge_list_.

void utility::graph::Graph::output_dimacs ( std::ostream &  os) const

describe this graph in dimacs form to the stream os.

writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out)

Parameters
os- [in] - the output stream to write to

References edge_list_, num_edges(), num_nodes_, and utility::graph::EdgeList::size().

void utility::graph::Graph::print_vertices ( ) const

send summary information to the screen for all vertices in the graph

calls print() on each of the nodes in the graph

References test.T200_Scoring::ii, nodes_, and num_nodes_.

void utility::graph::Graph::set_num_nodes ( platform::Size  num_nodes)

set the number of nodes in the graph – deletes any existing edges in the graph

alternative to integer constructor; first create an empty graph and later tell the graph how many nodes it has. If the graph is not already empty, it will delete everything its holding.

References create_new_node(), delete_everything(), test.T200_Scoring::ii, nodes_, num_nodes(), and num_nodes_.

Referenced by copy_connectivity(), and operator=().

Friends And Related Function Documentation

friend class Edge
friend
friend class Node
friend

Referenced by create_new_node().

Member Data Documentation

EdgeList utility::graph::Graph::edge_list_
private
boost::unordered_object_pool< EdgeListElement >* utility::graph::Graph::edge_list_element_pool_
private

the pool from which edge lists are to allocate their edge list elements

Referenced by edge_list_element_pool(), and ~Graph().

boost::unordered_object_pool< Edge >* utility::graph::Graph::edge_pool_
private

the pool from which class Graph allocates Edge objects. Not used by derived classes

Referenced by create_new_edge(), delete_edge(), and ~Graph().

Edge* utility::graph::Graph::focused_edge_
mutableprivate

Quick-access to a frequently needed edge – the most recently sought edge in a call to find_edge() or the most recently added edge.

Referenced by add_edge(), delete_everything(), drop_edge(), find_edge(), and focused_edge().

NodeVector utility::graph::Graph::nodes_
private
platform::Size utility::graph::Graph::num_edges_
private
platform::Size utility::graph::Graph::num_nodes_
private

The documentation for this class was generated from the following files: