Rosetta
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A Digraph with constant time edge insertion and deletion. Extensible. More...
#include <Digraph.hh>
Public Types | |
typedef utility::vector1< DirectedNode * > | DirectedNodeVector |
typedef DirectedNode::DirectedEdgeListIter | DirectedEdgeListIter |
typedef DirectedNode::DirectedEdgeListConstIter | DirectedEdgeListConstIter |
typedef utility::VirtualBase | parent |
Public Member Functions | |
DigraphCOP | get_self_ptr () const |
self pointers More... | |
DigraphOP | get_self_ptr () |
~Digraph () 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... | |
Digraph () | |
ctor More... | |
Digraph (platform::Size num_nodes) | |
num nodes ctor More... | |
Digraph (Digraph const &source) | |
copy ctor. Must not be called by derived class copy ctors. More... | |
Digraph & | operator= (Digraph const &source) |
assignment operator. source and this must have the same type. More... | |
void | copy_connectivity (Digraph 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... | |
void | add_node () |
Add a new node to the graph; preserve all of the existing edges in the graph. More... | |
DirectedEdge * | add_edge (platform::Size tail_node, platform::Size head_node) |
add a directed 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... | |
DirectedEdge * | add_edge (DirectedEdge 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 tail_node, platform::Size head_node) 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... | |
DirectedNode const * | get_node (platform::Size index) const |
DirectedNode * | get_node (platform::Size index) |
platform::Size | num_edges () const |
DirectedEdgeListConstIter | 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... | |
DirectedEdgeListIter | 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... | |
DirectedEdgeListConstIter | 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... | |
DirectedEdgeListIter | 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... | |
DirectedEdge * | find_edge (platform::Size tail_node, platform::Size head_node) |
returns a pointer to the directed edge connecting nodes tail_node and head_node, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval. More... | |
DirectedEdge const * | find_edge (platform::Size tail_node, platform::Size head_node) const |
returns a const pointer to the directed edge connecting nodes tail_node and head_node, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval. More... | |
DirectedEdge * | focused_edge () |
returns a pointer to the focused edge More... | |
DirectedEdge const * | focused_edge () const |
returns a const-pointer to the focused edge More... | |
virtual void | delete_edge (DirectedEdge *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... | |
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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 | |
VirtualBase & | operator= (VirtualBase const &)=default |
VirtualBase & | operator= (VirtualBase &&)=default |
Protected Member Functions | |
virtual platform::Size | count_static_memory () const |
virtual platform::Size | count_dynamic_memory () const |
void | drop_edge (DirectedEdgeListIter edge_iter) |
remove an edge from the entire-graph edge list. Called only by class DirectedEdge during its destructor More... | |
void | delete_everything () |
deallocate all nodes and edges from the graph More... | |
virtual DirectedNode * | create_new_node (platform::Size node_index) |
factory method for node creation, defined by derived graph classes, called by the base class More... | |
virtual DirectedEdge * | create_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 DirectedEdge * | create_new_edge (DirectedEdge 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< DirectedEdgeListElement > & | edge_list_element_pool () |
Used by class DirectedNode only, this is the pool from which edge lists are to allocate their edge lists elements from. More... | |
Private Attributes | |
platform::Size | num_nodes_ |
DirectedNodeVector | nodes_ |
platform::Size | num_edges_ |
boost::unordered_object_pool< DirectedEdgeListElement > * | edge_list_element_pool_ |
the pool from which edge lists are to allocate their edge list elements More... | |
DirectedEdgeList | edge_list_ |
boost::unordered_object_pool< DirectedEdge > * | edge_pool_ |
the pool from which class Digraph allocates DirectedEdge objects. Not used by derived classes More... | |
DirectedEdge * | focused_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 | DirectedNode |
class | DirectedEdge |
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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::Digraph::Digraph | ( | ) |
ctor
default constructor; creates an empty graph (no nodes, no edges)
Referenced by count_static_memory().
utility::graph::Digraph::Digraph | ( | platform::Size | num_nodes | ) |
num nodes ctor
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.
num_ig_nodes | - [in] - number of nodes that this graph will contain |
References create_new_node(), create_a3b_hbs::ii, nodes_, and num_nodes().
utility::graph::Digraph::Digraph | ( | Digraph 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 DirectedNode and DirectedEdge objects when it calls "create_new_node" and not DerivedDirectedNode or DerivedDirectedEdge 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::DirectedEdge::copy_from(), create_new_node(), find_edge(), create_a3b_hbs::ii, nodes_, and num_nodes_.
DirectedEdge * utility::graph::Digraph::add_edge | ( | DirectedEdge 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 Digraph 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::DirectedEdgeList::begin(), create_new_edge(), debug_assert, edge_list_, focused_edge_, get_edge_exists(), utility::graph::DirectedEdge::get_head_node_ind(), utility::graph::DirectedEdge::get_tail_node_ind(), num_edges_, utility::graph::DirectedEdgeList::push_front(), and utility::graph::DirectedEdge::set_pos_in_owners_list().
DirectedEdge * utility::graph::Digraph::add_edge | ( | platform::Size | tail_index, |
platform::Size | head_index | ||
) |
add a directed 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 tail_index and head_index. DirectedNodes 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.
tail_index | - [in] - index of one of the two nodes the edge is to connect |
head_index | - [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::DirectedEdgeList::last(), num_edges_, utility::graph::DirectedEdgeList::push_back(), and utility::graph::DirectedEdge::set_pos_in_owners_list().
Referenced by copy_connectivity(), Digraph(), and operator=().
void utility::graph::Digraph::add_node | ( | ) |
Add a new node to the graph; preserve all of the existing edges in the graph.
References create_new_node(), nodes_, and num_nodes_.
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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::DirectedEdgeList::const_begin(), and edge_list_.
Referenced by copy_connectivity(), Digraph(), and operator=().
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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::DirectedEdgeList::const_end(), and edge_list_.
Referenced by copy_connectivity(), Digraph(), and operator=().
void utility::graph::Digraph::copy_connectivity | ( | Digraph 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 EnergyDigraph into a Digraph)
References add_edge(), const_edge_list_begin(), const_edge_list_end(), drop_all_edges(), num_nodes_, and set_num_nodes().
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References num_edges_, and num_nodes_.
Referenced by getTotalMemoryUsage().
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References Digraph().
Referenced by getTotalMemoryUsage().
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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::DirectedEdge::get_head_node_ind(), and utility::graph::DirectedEdge::get_tail_node_ind().
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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().
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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 DirectedNode, and ObjexxFCL::index().
Referenced by add_node(), Digraph(), and set_num_nodes().
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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 delete_everything(), utility::graph::DirectedNode::drop_all_edges(), and drop_all_edges().
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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::DirectedEdgeList::begin(), delete_edge(), edge_list_, utility::graph::DirectedEdgeList::end(), focused_edge_, create_a3b_hbs::ii, nodes_, and num_nodes_.
Referenced by set_num_nodes(), and ~Digraph().
void utility::graph::Digraph::drop_all_edges | ( | ) |
delete all the edges present in the graph
deletes all edges in the graph
References utility::graph::DirectedEdgeList::begin(), delete_edge(), edge_list_, and utility::graph::DirectedEdgeList::end().
Referenced by copy_connectivity(), and operator=().
void utility::graph::Digraph::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
node | - [in] - index of the node |
References utility::graph::DirectedNode::drop_all_edges(), and get_node().
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remove an edge from the entire-graph edge list. Called only by class DirectedEdge 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.
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::DirectedEdgeList::erase(), focused_edge_, and num_edges_.
Referenced by utility::graph::DirectedEdge::~DirectedEdge().
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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::DirectedEdgeList::begin(), and edge_list_.
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Used by class DirectedNode only, this is the pool from which edge lists are to allocate their edge lists elements from.
References edge_list_element_pool_.
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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::DirectedEdgeList::end().
DirectedEdge * utility::graph::Digraph::find_edge | ( | platform::Size | tail_node, |
platform::Size | head_node | ||
) |
returns a pointer to the directed edge connecting nodes tail_node and head_node, 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 tail_node and head_node
graph keeps a pointer to the last edge that was accessed to that search is fairly efficient.
tail_node | - [in] - index of the first node |
head_node | - [in] - index of the second node |
References focused_edge_, nodes_, and utility::graph::DirectedEdge::same_edge().
Referenced by Digraph(), and get_edge_exists().
DirectedEdge const * utility::graph::Digraph::find_edge | ( | platform::Size | tail_node, |
platform::Size | head_node | ||
) | const |
returns a const pointer to the directed edge connecting nodes tail_node and head_node, 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 tail_node and head_node (const version)
graph keeps a pointer to the last edge that was accessed to that search is fairly efficient.
tail_node | - [in] - index of the tail node |
head_node | - [in] - index of the head node |
References focused_edge_, nodes_, and utility::graph::DirectedEdge::same_edge().
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returns a pointer to the focused edge
References focused_edge_.
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returns a const-pointer to the focused edge
References focused_edge_.
bool utility::graph::Digraph::get_edge_exists | ( | platform::Size | tail_node, |
platform::Size | head_node | ||
) | 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 tail_node and head_node exists
tail_node | - [in] - index of the one of the nodes |
head_node | - [in] - index of the other node |
References find_edge().
Referenced by add_edge().
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References debug_assert, nodes_, and num_nodes_.
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References debug_assert, nodes_, and num_nodes_.
Referenced by drop_all_edges_for_node().
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self pointers
platform::Size utility::graph::Digraph::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::DirectedEdgeList::const_begin(), utility::graph::DirectedEdgeList::const_end(), count_dynamic_memory(), count_static_memory(), edge_list_, create_a3b_hbs::ii, nodes_, and num_nodes().
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References num_edges_.
Referenced by output_dimacs().
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the number of nodes in the graph
References num_nodes_.
Referenced by Digraph(), getTotalMemoryUsage(), and set_num_nodes().
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 EnergyDigraph may be copied from another EnergyDigraph, but should not be copied from a Digraph.
References add_edge(), const_edge_list_begin(), const_edge_list_end(), drop_all_edges(), create_a3b_hbs::ii, nodes_, num_nodes_, and set_num_nodes().
void utility::graph::Digraph::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
os | - [in] - the output stream to write to |
References utility::graph::DirectedEdgeList::begin(), demo.D060_Folding::counter, edge_list_, and utility::graph::DirectedEdgeList::end().
void utility::graph::Digraph::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)
os | - [in] - the output stream to write to |
References utility::graph::DirectedEdgeList::begin(), edge_list_, utility::graph::DirectedEdgeList::end(), num_edges(), num_nodes_, and utility::graph::DirectedEdgeList::size().
void utility::graph::Digraph::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 create_a3b_hbs::ii, nodes_, and num_nodes_.
void utility::graph::Digraph::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(), create_a3b_hbs::ii, nodes_, num_nodes(), and num_nodes_.
Referenced by copy_connectivity(), and operator=().
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Referenced by create_new_node().
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the pool from which edge lists are to allocate their edge list elements
Referenced by edge_list_element_pool(), and ~Digraph().
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the pool from which class Digraph allocates DirectedEdge objects. Not used by derived classes
Referenced by create_new_edge(), delete_edge(), and ~Digraph().
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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().
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Referenced by add_edge(), count_dynamic_memory(), drop_edge(), and num_edges().
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