org.biomage.Description
Class OntologyEntry

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Description.OntologyEntry

All Implemented Interfaces:

HasOntologyReference, HasPropertySets, java.io.Serializable

public class OntologyEntry

extends Extendable

implements java.io.Serializable, HasOntologyReference

A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name', value could be 'homo sapiens' and ontology would be taxonomy database, NCBI.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected DatabaseEntry

ontologyReference Many ontology entries will not yet have formalized ontologies.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

OntologyEntry()
Default constructor.

OntologyEntry(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

java.lang.String	getCategory() Get method for category
java.lang.String	getDescription() Get method for description
DatabaseEntry	getOntologyReference() Get method for ontologyReference
java.lang.String	getValue() Get method for value
void	setCategory(java.lang.String category) Set method for category
void	setDescription(java.lang.String description) Set method for description
void	setOntologyReference(DatabaseEntry ontologyReference) Set method for ontologyReference
void	setValue(java.lang.String value) Set method for value
void	writeAssociations(java.io.Writer out) writeAssociations This method is responsible for assembling the association data into XML.
void	writeAttributes(java.io.Writer out) writeAttributes This method is responsible for assembling the attribute data into XML.
void	writeMAGEML(java.io.Writer out) writeMAGEML This method is responsible for assembling the attribute and association data into XML.

Methods inherited from class org.biomage.Common.Extendable

addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

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

Field Detail

ontologyReference

protected DatabaseEntry ontologyReference

Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference.

Constructor Detail

OntologyEntry

public OntologyEntry()

Default constructor.

OntologyEntry

public OntologyEntry(org.xml.sax.Attributes atts)

Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException

writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:

writeMAGEML in class Extendable

java.io.IOException

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException

writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:

writeAttributes in class Extendable

java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException

writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:

writeAssociations in class Extendable

java.io.IOException

setCategory

public void setCategory(java.lang.String category)

Set method for category

getCategory

public java.lang.String getCategory()

Get method for category

Returns:

value of the attribute

setValue

public void setValue(java.lang.String value)

Set method for value

Parameters:

value - to set

getValue

public java.lang.String getValue()

Get method for value

Returns:

value of the attribute

setDescription

public void setDescription(java.lang.String description)

Set method for description

getDescription

public java.lang.String getDescription()

Get method for description

Returns:

value of the attribute

setOntologyReference

public void setOntologyReference(DatabaseEntry ontologyReference)

Set method for ontologyReference

Specified by:

setOntologyReference in interface HasOntologyReference

getOntologyReference

public DatabaseEntry getOntologyReference()

Get method for ontologyReference

Specified by:

getOntologyReference in interface HasOntologyReference

Returns:

value of the attribute