org.metaqtl.bio.entity
Class Ontology

java.lang.Object
  org.metaqtl.bio.entity.BioEntity
      org.metaqtl.bio.entity.Ontology

All Implemented Interfaces:

IBioAdaptable, IBioEntity, IBioOntology

public class Ontology
extends BioEntity
implements IBioOntology

Field Summary

Fields inherited from class org.metaqtl.bio.entity.BioEntity

name, parent, properties

Constructor Summary

Ontology()

Method Summary

IBioAdapter	getBioAdapter()
java.lang.String	getFunction() Returns the function of the ontology
IBioOntologyTerm	getRoot() Returns the root of the ontology tree.
IBioOntologyTerm	getTerm(IBioOntologyTerm term) Returns if exists the term in the ontology which matches the given one.
IBioOntologyTerm	getTerm(java.lang.String termName) This method looks into the ontology if there is a term with the given name and returns it.
int	getType() There are 2 main class of entities.
void	setFunction(java.lang.String function) Set the function of the ontology.
void	setRoot(IBioOntologyTerm root) Sets the root of the ontology.
void	setRoot(OntologyTerm root)

Methods inherited from class org.metaqtl.bio.entity.BioEntity

getName, getParent, getProperties, newBioEntity, setName, setProperties

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.metaqtl.bio.IBioEntity

getName, getParent, getProperties, setName, setProperties

Constructor Detail

Ontology

public Ontology()

Method Detail

setFunction

public void setFunction(java.lang.String function)

Set the function of the ontology.

Parameters:

function -

getFunction

public java.lang.String getFunction()

Description copied from interface: IBioOntology

Returns the function of the ontology

Specified by:

getFunction in interface IBioOntology

Returns:

getRoot

public IBioOntologyTerm getRoot()

Description copied from interface: IBioOntology

Returns the root of the ontology tree.

Specified by:

getRoot in interface IBioOntology

Returns:

the root of the ontology tree.

getTerm

public IBioOntologyTerm getTerm(IBioOntologyTerm term)

Description copied from interface: IBioOntology

Returns if exists the term in the ontology which matches the given one.

Specified by:

getTerm in interface IBioOntology

Parameters:

term - the term to look for in the ontology.

Returns:

the term if found, null otherwise.

getType

public int getType()

Description copied from interface: IBioEntity

There are 2 main class of entities. The first one deals with population biological entity, i.e population itself and individuals. The second class is a representation of microscopic biological entity from genome container to alleles.

Specified by:

getType in interface IBioEntity

Specified by:

getType in class BioEntity

getBioAdapter

public IBioAdapter getBioAdapter()

Specified by:

getBioAdapter in interface IBioAdaptable

setRoot

public void setRoot(IBioOntologyTerm root)

Description copied from interface: IBioOntology

Sets the root of the ontology.

Specified by:

setRoot in interface IBioOntology

Parameters:

root - the root of the ontology

setRoot

public void setRoot(OntologyTerm root)

Parameters:

root - the root of the ontology.

getTerm

public IBioOntologyTerm getTerm(java.lang.String termName)

Description copied from interface: IBioOntology

This method looks into the ontology if there is a term with the given name and returns it.

Specified by:

getTerm in interface IBioOntology

Parameters:

termName - the name of the term to find.

Returns:

the term or null if not found.