org.thalia.bio
Interface IBioOntology

All Superinterfaces:
IBioAdaptable, IBioEntity
All Known Implementing Classes:
Ontology

public interface IBioOntology
extends IBioEntity

This interface defines some rules to handle a ontology. Here we assume that the onotlogy can be represented by a simple directed acyclic graph, i.e a parent-child linking between the concepts (if A is child of B then B can't be a child of A).


Method Summary
 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.
 void setRoot(IBioOntologyTerm root)
          Sets the root of the ontology.
 
Methods inherited from interface org.thalia.bio.IBioEntity
getName, getParent, getProperties, getType, setName, setProperties
 
Methods inherited from interface org.thalia.bio.IBioAdaptable
getBioAdapter
 

Method Detail

getFunction

java.lang.String getFunction()
Returns the function of the ontology

Returns:

getRoot

IBioOntologyTerm getRoot()
Returns the root of the ontology tree.

Returns:
the root of the ontology tree.

setRoot

void setRoot(IBioOntologyTerm root)
Sets the root of the ontology.

Parameters:
root - the root of the ontology

getTerm

IBioOntologyTerm getTerm(IBioOntologyTerm term)
Returns if exists the term in the ontology which matches the given one.

Parameters:
term - the term to look for in the ontology.
Returns:
the term if found, null otherwise.

getTerm

IBioOntologyTerm getTerm(java.lang.String termName)
This method looks into the ontology if there is a term with the given name and returns it.

Parameters:
termName - the name of the term to find.
Returns:
the term or null if not found.