DAG< NodeType > Class Template Reference

#include <dag.h>

List of all members.

Public Member Functions
	DAG ()
	DAG (const DAG< NodeType > &rhs)
	DAG (istream *in)
virtual	~DAG ()
const DAG< NodeType > &	operator= (const DAG &rhs)
void	clear ()
virtual void	addNode (NodeType *node)
void	computeDifference (DAG< NodeType > &other, DAG< NodeType > &difference)
virtual void	computePower (unsigned int exponent, DAG< NodeType > &powerDAG)
virtual void	computeLeaves (vector< NodeType * > &leaves, unsigned int type=0)
virtual void	computeRoots (vector< NodeType * > &roots, unsigned int type=0)
virtual void	computeTopologicalSort (vector< NodeType * > &sortedFunctions, unsigned int type=0)
virtual void	computeTransitiveClosure (DAG< NodeType > &closedDAG)
virtual void	computeTransitiveReduction (DAG< NodeType > &reducedDAG)
unsigned int	getNumEdges () const
unsigned int	getNumNodes () const
void	print (string file) const
void	print (ostream &ostr) const
	DAG ()
	DAG (const DAG< NodeType > &rhs)
	DAG (istream *in)
virtual	~DAG ()
const DAG< NodeType > &	operator= (const DAG &rhs)
void	clear ()
virtual void	addNode (NodeType *node)
void	computeDifference (DAG< NodeType > &other, DAG< NodeType > &difference)
virtual void	computePower (unsigned int exponent, DAG< NodeType > &powerDAG)
virtual void	computeLeaves (vector< NodeType * > &leaves, unsigned int type=0)
virtual void	computeRoots (vector< NodeType * > &roots, unsigned int type=0)
virtual void	computeTopologicalSort (vector< NodeType * > &sortedFunctions, unsigned int type=0)
virtual void	computeTransitiveClosure (DAG< NodeType > &closedDAG)
virtual void	computeTransitiveReduction (DAG< NodeType > &reducedDAG)
unsigned int	getNumEdges () const
unsigned int	getNumNodes () const
void	print (string file) const
void	print (ostream &ostr) const
Protected Member Functions
void	_copy (const DAG< NodeType > &rhs)
void	_copyNodes (const DAG< NodeType > &rhs)
unsigned int	_getNodeIndex (const NodeType *node) const
void	_copy (const DAG< NodeType > &rhs)
void	_copyNodes (const DAG< NodeType > &rhs)
unsigned int	_getNodeIndex (const NodeType *node) const
Protected Attributes
vector< NodeType * >	_nodes
map< const NodeType *, unsigned int >	_nodesToIndices

---

Detailed Description

template<typename NodeType>
class DAG< NodeType >

A class that encapsulates a Directed Acyclic Graph. NodeType is a class that stores information for a particular node. In a particular instantiation of DAG, NodeType should be a subclass of DAGNode.

---

Constructor & Destructor Documentation

template<typename NodeType>

DAG< NodeType >::DAG

(

)

[inline]

Constructor

template<typename NodeType>

DAG< NodeType >::DAG

(

const DAG< NodeType > &

rhs

)

[inline]

Copy constructor

template<typename NodeType>

DAG< NodeType >::DAG

(

istream *

in

)

Constructor

Parameters:

*in	A stream pointer (eg: &cout, &infile, &myStringStream)

template<typename NodeType>

virtual DAG< NodeType >::~DAG

(

)

[inline, virtual]

Destructor

template<typename NodeType>

DAG< NodeType >::DAG

(

)

[inline]

Constructor

template<typename NodeType>

DAG< NodeType >::DAG

(

const DAG< NodeType > &

rhs

)

[inline]

Copy constructor

template<typename NodeType>

DAG< NodeType >::DAG

(

istream *

in

)

Constructor

Parameters:

*in	A stream pointer (eg: &cout, &infile, &myStringStream)

template<typename NodeType>

virtual DAG< NodeType >::~DAG

(

)

[inline, virtual]

Destructor

---

Member Function Documentation

template<typename NodeType>

virtual void DAG< NodeType >::addNode

(

NodeType *

node

)

[inline, virtual]

Adds a node to the DAG.

Note:

The DAG does not manage the storage of the added nodes. The calling method is responsible for allocating and deallocating storage. The DAG simply stores the pointers to the nodes in the DAG.

template<typename NodeType>

virtual void DAG< NodeType >::addNode

(

NodeType *

node

)

[inline, virtual]

Adds a node to the DAG.

Note:

The DAG does not manage the storage of the added nodes. The calling method is responsible for allocating and deallocating storage. The DAG simply stores the pointers to the nodes in the DAG.

template<typename NodeType>

void DAG< NodeType >::clear

(

)

[inline]

Clears memory used by the DAG.

template<typename NodeType>

void DAG< NodeType >::clear

(

)

[inline]

Clears memory used by the DAG.

template<typename NodeType>

void DAG< NodeType >::computeDifference	(	DAG< NodeType > &	other,
		DAG< NodeType > &	difference
	)

Adds a node to the DAG.

Note:

The DAG does not manage the storage of the added nodes. The calling method is responsible for allocating and deallocating storage. The DAG simply stores the pointers to the nodes in the DAG. Computes the difference between the invocant and other.

Parameters:

[in]	other,an	instance of DAG< NodeType >
[out]	difference,an	instance of DAG< NodeType > that will hold the difference between the invocant and other.

The method adds those parent-child relations to difference that are in the invocant but not in other.

Warning:

The method requires that the invocant and other have exactly the same set of nodes and that the nodes be added to both DAGs in precisely the same order. You can meet this requirement if you constructed the invocant by assigning other to it or by invoking the copy constructor on other or vice-versa. This onerous requirement may go away in the future.

template<typename NodeType>

void DAG< NodeType >::computeDifference	(	DAG< NodeType > &	other,
		DAG< NodeType > &	difference
	)

Adds a node to the DAG.

Note:

The DAG does not manage the storage of the added nodes. The calling method is responsible for allocating and deallocating storage. The DAG simply stores the pointers to the nodes in the DAG. Computes the difference between the invocant and other.

Parameters:

[in]	other,an	instance of DAG< NodeType >
[out]	difference,an	instance of DAG< NodeType > that will hold the difference between the invocant and other.

The method adds those parent-child relations to difference that are in the invocant but not in other.

Warning:

The method requires that the invocant and other have exactly the same set of nodes and that the nodes be added to both DAGs in precisely the same order. You can meet this requirement if you constructed the invocant by assigning other to it or by invoking the copy constructor on other or vice-versa. This onerous requirement may go away in the future.

template<typename NodeType>

void DAG< NodeType >::computeLeaves	(	vector< NodeType * > &	leaves,
		unsigned int	type = 0
	)		[virtual]

Compute the leaves of the DAG, i.e., nodes without any children.

template<typename NodeType>

virtual void DAG< NodeType >::computeLeaves	(	vector< NodeType * > &	leaves,
		unsigned int	type = 0
	)		[virtual]

Compute the leaves of the DAG, i.e., nodes without any children.

template<typename NodeType>

void DAG< NodeType >::computePower	(	unsigned int	exponent,
		DAG< NodeType > &	powerDAG
	)		[virtual]

Computes the kth power of the DAG.

Parameters:

[in]	exponent,the	value of the power to compute.
[out]	powerDAG,an	instance of DAG< NodeType > that will contain the power.

The kth power of a DAG is another DAG that contains an edge between nodes a and b if the there is a path of length k between the nodes in the original DAG. For example, the first power of a DAG is the DAG itself and the second power of a DAG connects each node to all its grandparents in the original DAG. The union of all powers of a DAG is the transitive closure of the DAG.

template<typename NodeType>

virtual void DAG< NodeType >::computePower	(	unsigned int	exponent,
		DAG< NodeType > &	powerDAG
	)		[virtual]

Computes the kth power of the DAG.

Parameters:

[in]	exponent,the	value of the power to compute.
[out]	powerDAG,an	instance of DAG< NodeType > that will contain the power.

The kth power of a DAG is another DAG that contains an edge between nodes a and b if the there is a path of length k between the nodes in the original DAG. For example, the first power of a DAG is the DAG itself and the second power of a DAG connects each node to all its grandparents in the original DAG. The union of all powers of a DAG is the transitive closure of the DAG.

template<typename NodeType>

void DAG< NodeType >::computeRoots	(	vector< NodeType * > &	roots,
		unsigned int	type = 0
	)		[virtual]

Compute the roots of the DAG, i.e., nodes without any parents.

template<typename NodeType>

virtual void DAG< NodeType >::computeRoots	(	vector< NodeType * > &	roots,
		unsigned int	type = 0
	)		[virtual]

Compute the roots of the DAG, i.e., nodes without any parents.

template<typename NodeType>

void DAG< NodeType >::computeTopologicalSort	(	vector< NodeType * > &	sortedFunctions,
		unsigned int	type = 0
	)		[virtual]

Performs a topological sort of the functions in the DAG from the root downward.

The nodes in each connected component of the DAG appear consecutively in the sorted order.

Parameters:

sortedFunction,a	reference to a vector of pointers to instance of NodeType. The method fills this vector with the sorted list of functions.
type,an	integer defining what type of relations to use when performing the topological sort.

template<typename NodeType>

virtual void DAG< NodeType >::computeTopologicalSort	(	vector< NodeType * > &	sortedFunctions,
		unsigned int	type = 0
	)		[virtual]

Performs a topological sort of the functions in the DAG from the root downward.

The nodes in each connected component of the DAG appear consecutively in the sorted order.

Parameters:

sortedFunction,a	reference to a vector of pointers to instance of NodeType. The method fills this vector with the sorted list of functions.
type,an	integer defining what type of relations to use when performing the topological sort.

template<typename NodeType>

void DAG< NodeType >::computeTransitiveClosure

(

DAG< NodeType > &

closedDAG

)

[virtual]

Compute the transitive closure of the DAG.

Parameters:

[out]

closedDAG,the

computed transitive closure.

For every pair of nodes a and b in the invocant such that b is an ancestor of a, the methods adds b as a parent of a in the transitive closure.

template<typename NodeType>

virtual void DAG< NodeType >::computeTransitiveClosure

(

DAG< NodeType > &

closedDAG

)

[virtual]

Compute the transitive closure of the DAG.

Parameters:

[out]

closedDAG,the

computed transitive closure.

For every pair of nodes a and b in the invocant such that b is an ancestor of a, the methods adds b as a parent of a in the transitive closure.

template<typename NodeType>

void DAG< NodeType >::computeTransitiveReduction

(

DAG< NodeType > &

reducedDAG

)

[virtual]

Compute the transitive reduction of the DAG.

Parameters:

[out]

reducedDAG,the

computed transitive reduction.

For every pair of nodes a and b in the invocant such that b is a parent of a, the methods ensures that b is an ancestor of a in the transitive reduction. The method includes all edges in the invocant in the reduction that are not edges in the square of the invocant.

Note:

The method works correctly if and only if the invocant is transitively closed.

template<typename NodeType>

virtual void DAG< NodeType >::computeTransitiveReduction

(

DAG< NodeType > &

reducedDAG

)

[virtual]

Compute the transitive reduction of the DAG.

Parameters:

[out]

reducedDAG,the

computed transitive reduction.

For every pair of nodes a and b in the invocant such that b is a parent of a, the methods ensures that b is an ancestor of a in the transitive reduction. The method includes all edges in the invocant in the reduction that are not edges in the square of the invocant.

Note:

The method works correctly if and only if the invocant is transitively closed.

template<typename NodeType >

unsigned int DAG< NodeType >::getNumEdges

(

)

const

Reads information about the Gene Ontology.

Parameters:

file	A string containing the location of a file. Reads information about the DAG.
*in	A stream pointer (eg: &cout, &infile, &myStringStream) Performs a transitive closure traversal of the DAG to determine the ancestors of each node.

Partial traversals are cached making this a constant time operation when repeated and fast if some of the ancestors have already been computed

Parameters:

obj	A gene ontology function object pointer
type	an integer defining what type of traversal will be done: 0 means any parent relation (currently is_a and part_of) 1 means follow only is_a relations 2 means follow only part_of relations

Returns:

A set of ancestors of the type specified

Returns a node's direct parents

Parameters:

obj	A pointer to an instance of NodeType.
type	an integer defining what type of parents to return: 0 means any parent relation (currently is_a and part_of) 1 means only is_a relations 2 means only part_of relations

Returns:

A set of parents of the type specified

Performs a transitive closure traversal of the DAG to determine the descendants of each function.

Partial traversals are cached making this a constant time operation when repeated and fast if some of the descendants have already been computed.

Parameters:

obj	A pointer to an instance of NodeType.
type	an integer defining what type of traversal will be done: 0 means any descendant relation (currently is_a and part_of) 1 means follow only is_a relations 2 means follow only part_of relations

Returns:

A set of descendants of the type specified

Returns a node's direct children

Parameters:

obj	A pointer to an instance of NodeType.
type	an integer defining what type of children to return: 0 means any child relation (currently is_a and part_of) 1 means only is_a relations 2 means only part_of relations

Returns:

A set of children of the type specified

Constant time lookup of function by id (or alternative id)

Parameters:

id	The id to lookup

Returns:

a go function pointer that has that id Constant time lookup of function by id (or alternative id)

Parameters:

id	The id to lookup. This id is a string.

Returns:

a go function pointer that has that id.

The method converts id to an integer to removing any prefix of the form "GO:" Return the number of edges (parent-child relationships) in the DAG.

template<typename NodeType>

unsigned int DAG< NodeType >::getNumEdges

(

)

const

Reads information about the Gene Ontology.

Parameters:

file	A string containing the location of a file. Reads information about the DAG.
*in	A stream pointer (eg: &cout, &infile, &myStringStream) Performs a transitive closure traversal of the DAG to determine the ancestors of each node.

Partial traversals are cached making this a constant time operation when repeated and fast if some of the ancestors have already been computed

Parameters:

obj	A gene ontology function object pointer
type	an integer defining what type of traversal will be done: 0 means any parent relation (currently is_a and part_of) 1 means follow only is_a relations 2 means follow only part_of relations

Returns:

A set of ancestors of the type specified

Returns a node's direct parents

Parameters:

obj	A pointer to an instance of NodeType.
type	an integer defining what type of parents to return: 0 means any parent relation (currently is_a and part_of) 1 means only is_a relations 2 means only part_of relations

Returns:

A set of parents of the type specified

Performs a transitive closure traversal of the DAG to determine the descendants of each function.

Partial traversals are cached making this a constant time operation when repeated and fast if some of the descendants have already been computed.

Parameters:

obj	A pointer to an instance of NodeType.
type	an integer defining what type of traversal will be done: 0 means any descendant relation (currently is_a and part_of) 1 means follow only is_a relations 2 means follow only part_of relations

Returns:

A set of descendants of the type specified

Returns a node's direct children

Parameters:

obj	A pointer to an instance of NodeType.
type	an integer defining what type of children to return: 0 means any child relation (currently is_a and part_of) 1 means only is_a relations 2 means only part_of relations

Returns:

A set of children of the type specified

Constant time lookup of function by id (or alternative id)

Parameters:

id	The id to lookup

Returns:

a go function pointer that has that id Constant time lookup of function by id (or alternative id)

Parameters:

id	The id to lookup. This id is a string.

Returns:

a go function pointer that has that id.

The method converts id to an integer to removing any prefix of the form "GO:" Return the number of edges (parent-child relationships) in the DAG.

template<typename NodeType>

unsigned int DAG< NodeType >::getNumNodes

(

)

const

Return the number of nodes in the DAG.

template<typename NodeType >

unsigned int DAG< NodeType >::getNumNodes

(

)

const

Return the number of nodes in the DAG.

template<typename NodeType>

const DAG< NodeType >& DAG< NodeType >::operator=

(

const DAG< NodeType > &

rhs

)

[inline]

Assignment operator

template<typename NodeType>

const DAG< NodeType >& DAG< NodeType >::operator=

(

const DAG< NodeType > &

rhs

)

[inline]

Assignment operator

template<typename NodeType >

void DAG< NodeType >::print

(

string

file

)

const

Print the edges of the DAG to the output file.

The method outputs the edges of the DAG in tab-delimited form. Each line contains the id of a child node and the id of a parent node separated by a tab.

template<typename NodeType>

void DAG< NodeType >::print

(

string

file

)

const

Print the edges of the DAG to the output file.

The method outputs the edges of the DAG in tab-delimited form. Each line contains the id of a child node and the id of a parent node separated by a tab.

template<typename NodeType >

void DAG< NodeType >::print

(

ostream &

ostr

)

const

Print the edges of the DAG to the output stream.

The method outputs the edges of the DAG in tab-delimited form. Each line contains the id of a child node and the id of a parent node separated by a tab.

template<typename NodeType>

void DAG< NodeType >::print

(

ostream &

ostr

)

const

Print the edges of the DAG to the output stream.

The method outputs the edges of the DAG in tab-delimited form. Each line contains the id of a child node and the id of a parent node separated by a tab.

---

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

• /home/poirel/src/c++/biorithm/libapriori/dag.h
• /home/poirel/src/c++/biorithm/truth-tables/dag.h