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org.biomage.Description
Class OntologyEntry  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Description.OntologyEntry

All Implemented Interfaces:

org.biomage.Interface.HasOntologyReference, org.biomage.Interface.HasPropertySets, java.io.Serializable

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public class OntologyEntry

extends org.biomage.Common.Extendable

implements java.io.Serializable, org.biomage.Interface.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.

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Nested Class Summary

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
(package private)  java.lang.String	category           The category to which this entry belongs.
(package private)  java.lang.String	description           The description of the meaning for this entry.
private  DatabaseEntry	ontologyReference           Many ontology entries will not yet have formalized ontologies.
(package private)  java.lang.String	value           The value for this entry in this category.

 

Fields inherited from class org.biomage.Common.Extendable

 

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
void	writeAttributes(java.io.Writer out)           writeAttributes
void	writeMAGEML(java.io.Writer out)           writeMAGEML

 

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

category

java.lang.String category

The category to which this entry belongs.

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value

java.lang.String value

The value for this entry in this category.

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description

java.lang.String description

The description of the meaning for this entry.

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ontologyReference

private 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.

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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.

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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.

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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.

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setCategory

public void setCategory(java.lang.String category)

Set method for category

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getCategory

public java.lang.String getCategory()

Get method for category

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setValue

public void setValue(java.lang.String value)

Set method for value

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getValue

public java.lang.String getValue()

Get method for value

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setDescription

public void setDescription(java.lang.String description)

Set method for description

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getDescription

public java.lang.String getDescription()

Get method for description

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setOntologyReference

public void setOntologyReference(DatabaseEntry ontologyReference)

Set method for ontologyReference

Specified by:

setOntologyReference in interface org.biomage.Interface.HasOntologyReference

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getOntologyReference

public DatabaseEntry getOntologyReference()

Get method for ontologyReference

Specified by:

getOntologyReference in interface org.biomage.Interface.HasOntologyReference

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