GOFunction Class Reference

#include <GO.h>

Inheritance diagram for GOFunction:

List of all members.

Public Member Functions
	GOFunction ()
	GOFunction (string cat, string id, string name="")
virtual	~GOFunction ()
void	_init ()
MyNT	computeSemanticValue () const
	Compute the semantic value of a function.
unsigned int	computeSiblings (unsigned int type=0)
	Compute the siblings the the invocant.
int	getIntegerId ()
vector< int >	getAltIds ()
vector< string >	getSubsets ()
vector< string >	getSynonyms ()
vector< string >	getXrefAnalogs ()
string	getNamespace ()
string	getDef ()
string	getComment ()
bool	isObsolete ()
virtual unsigned int	getNumParents (int type=0)
virtual unsigned int	getNumChildren (int type=0)
virtual set< GOFunction * >	getAncestors (int type=0)
virtual map< GOFunction *, unsigned int >	getAncestorsWithDistance (int type=0)
virtual set< GOFunction * >	getChildren (int type=0)
virtual set< GOFunction * >	getDescendants (int type=0)
virtual map< GOFunction *, unsigned int >	getDescendantsWithDistance (int type=0)
virtual unsigned int	getDistanceToAncestor (GOFunction *ancestor, unsigned int type=0)
	Return the distance from the invocant to an ancestor.
virtual unsigned int	getDistanceToDescendant (GOFunction *descendant, unsigned int type=0)
	Return the distance from the invocant to a descendant.
virtual set< GOFunction * >	getParents (int type=0)
set< GOFunction * >	getSiblings (unsigned int type=0)
	Return the siblings of the function.
bool	isAncestor (GOFunction *candidate)
bool	isChild (GOFunction *candidate)
	Returns true if candidate is a parent of the invocant.
bool	isDescendant (GOFunction *candidate)
bool	isParent (GOFunction *candidate)
	Returns true if candidate is a parent of the invocant.
void	addDepth (unsigned int depth, int type=0)
set< unsigned int >	getDepths (int type=0)
	Return all the depths of the function as a set of unsigned integers.
unsigned int	getMinimumDepth (int type=0)
	Return the minimum depth of the function.
unsigned int	getMaximumDepth (int type=0)
	Return the maximum depth of the function.
Protected Member Functions
unsigned int	_computeSiblingsNaively (unsigned int type=0)
Friends
class	GeneOntology

---

Detailed Description

An object that represents a single go function which should only be created through a GeneOntology object

---

Constructor & Destructor Documentation

GOFunction::GOFunction

(

)

[inline]

Constructor

virtual GOFunction::~GOFunction

(

)

[inline, virtual]

Destructor

---

Member Function Documentation

MyNT GOFunction::computeSemanticValue

(

)

const

Compute the semantic value of a function.

unsigned int GOFunction::computeSiblings

(

unsigned int

type = 0

)

Compute the siblings the the invocant.

A sibling is a function that is a descendant of an ancestor of the invocant and an ancestor of a descendant of the invocant.

vector<int> GOFunction::getAltIds

(

)

[inline]

Accessor for alternative ids

Returns:

vector of function id alternatives (empty vector if no alternatives exist)

string GOFunction::getComment

(

)

[inline]

Accessor for comment

Returns:

function comment (empty string if no comment exists)

string GOFunction::getDef

(

)

[inline]

Accessor for def

Returns:

function definition (empty string if none exists)

unsigned int GOFunction::getDistanceToAncestor	(	GOFunction *	ancestor,
		unsigned int	type = 0
	)		[virtual]

Return the distance from the invocant to an ancestor.

Parameters:

[in]

ancestor,a

pointer to an instance of GOFunction.

isAncestor(ancestor, type) returns true.

unsigned int GOFunction::getDistanceToDescendant	(	GOFunction *	descendant,
		unsigned int	type = 0
	)		[virtual]

Return the distance from the invocant to a descendant.

Parameters:

[in]

descendant,a

pointer to an instance of GOFunction.

isDescendant(descendant, type) returns true.

int GOFunction::getIntegerId

(

)

[inline]

Accessor for INTEGERID

Returns:

function id

string GOFunction::getNamespace

(

)

[inline]

Accessor for name

Returns:

function name

Accessor for namespace

Returns:

function namespace (eg: Biological Function) - uses GeneOntology default namespace if none exist

set< GOFunction * > GOFunction::getSiblings

(

unsigned int

type = 0

)

[inline]

Return the siblings of the function.

The method computes the siblings of the function if they have not yet been computed by a previous call to GOFunction::computeSiblings().

vector<string> GOFunction::getSubsets

(

)

[inline]

Accessor for subsets

Returns:

vector of function subsets (what are subsets good for?)

vector<string> GOFunction::getSynonyms

(

)

[inline]

Accessor for synonyms

Returns:

vector of function name synonyms (empty vector if none exist)

vector<string> GOFunction::getXrefAnalogs

(

)

[inline]

Accessor for xref analogs

Returns:

vector of function xref analogs as strings (empty vector if none exist) - leaves parsing of these to user code

bool GOFunction::isAncestor

(

GOFunction *

candidate

)

[inline]

Returns true if candidate is an ancestor of the invocant.

bool GOFunction::isDescendant

(

GOFunction *

candidate

)

[inline]

Returns true if candidate is a descendant of the invocant.

bool GOFunction::isObsolete

(

)

[inline]

Accessor for obsolete

Returns:

true if function is obsolete, false otherwise

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

• /home/poirel/src/c++/biorithm/libfun/GO.h
• /home/poirel/src/c++/biorithm/libfun/GO.C