org.thalia.bio.entity
Class Ontology

java.lang.Object
  extended by org.thalia.bio.entity.BioEntity
      extended by org.thalia.bio.entity.Ontology
All Implemented Interfaces:
IBioAdaptable, IBioEntity, IBioOntology

public class Ontology
extends BioEntity
implements IBioOntology


Field Summary
 
Fields inherited from class org.thalia.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.thalia.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.thalia.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.