org.biomage.Description
Class Description

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

All Implemented Interfaces:

HasAnnotations, HasAuditTrail, HasBibliographicReferences, HasDatabaseReferences, HasDescriptions, HasExternalReference, HasPropertySets, HasSecurity, java.io.Serializable

public class Description

extends Describable

implements java.io.Serializable, HasDatabaseReferences, HasBibliographicReferences, HasExternalReference, HasAnnotations

A free text description of an object.

See Also:

Serialized Form

Nested Class Summary

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

HasDatabaseReferences.DatabaseReferences_list

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

HasBibliographicReferences.BibliographicReferences_list

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

HasAnnotations.Annotations_list

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasAnnotations.Annotations_list	annotations Allows specification of ontology entries related to the instance being described.
protected HasBibliographicReferences.BibliographicReferences_list	bibliographicReferences References to existing literature.
protected HasDatabaseReferences.DatabaseReferences_list	databaseReferences References to entries in databases.
protected ExternalReference	externalReference Specifies where the described instance was originally obtained from.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Description()
Default constructor.

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

Method Summary

void	addToAnnotations(int position, OntologyEntry ontologyEntry) Method to add OntologyEntry at position to Annotations_list
void	addToAnnotations(OntologyEntry ontologyEntry) Method to add OntologyEntry to Annotations_list
void	addToBibliographicReferences(BibliographicReference bibliographicReference) Method to add BibliographicReference to BibliographicReferences_list
void	addToBibliographicReferences(int position, BibliographicReference bibliographicReference) Method to add BibliographicReference at position to BibliographicReferences_list
void	addToDatabaseReferences(DatabaseEntry databaseEntry) Method to add DatabaseEntry to DatabaseReferences_list
void	addToDatabaseReferences(int position, DatabaseEntry databaseEntry) Method to add DatabaseEntry at position to DatabaseReferences_list
HasAnnotations.Annotations_list	getAnnotations() Get method for annotations
HasBibliographicReferences.BibliographicReferences_list	getBibliographicReferences() Get method for bibliographicReferences
HasDatabaseReferences.DatabaseReferences_list	getDatabaseReferences() Get method for databaseReferences
ExternalReference	getExternalReference() Get method for externalReference
OntologyEntry	getFromAnnotations(int position) Method to get OntologyEntry from Annotations_list
BibliographicReference	getFromBibliographicReferences(int position) Method to get BibliographicReference from BibliographicReferences_list
DatabaseEntry	getFromDatabaseReferences(int position) Method to get DatabaseEntry from DatabaseReferences_list
java.lang.String	getText() Get method for text
void	removeElementAtFromAnnotations(int position) Method to remove by position from Annotations_list
void	removeElementAtFromBibliographicReferences(int position) Method to remove by position from BibliographicReferences_list
void	removeElementAtFromDatabaseReferences(int position) Method to remove by position from DatabaseReferences_list
void	removeFromAnnotations(OntologyEntry ontologyEntry) Method to remove first OntologyEntry from Annotations_list
void	removeFromBibliographicReferences(BibliographicReference bibliographicReference) Method to remove first BibliographicReference from BibliographicReferences_list
void	removeFromDatabaseReferences(DatabaseEntry databaseEntry) Method to remove first DatabaseEntry from DatabaseReferences_list
void	setAnnotations(HasAnnotations.Annotations_list annotations) Set method for annotations
void	setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list bibliographicReferences) Set method for bibliographicReferences
void	setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list databaseReferences) Set method for databaseReferences
void	setExternalReference(ExternalReference externalReference) Set method for externalReference
void	setText(java.lang.String text) Set method for text
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.Describable

addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity

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

externalReference

protected ExternalReference externalReference

Specifies where the described instance was originally obtained from.

annotations

protected HasAnnotations.Annotations_list annotations

Allows specification of ontology entries related to the instance being described.

databaseReferences

protected HasDatabaseReferences.DatabaseReferences_list databaseReferences

References to entries in databases.

bibliographicReferences

protected HasBibliographicReferences.BibliographicReferences_list bibliographicReferences

References to existing literature.

Constructor Detail

Description

public Description()

Default constructor.

Description

public Description(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 Describable

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 Describable

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 Describable

java.io.IOException

setText

public void setText(java.lang.String text)

Set method for text

getText

public java.lang.String getText()

Get method for text

Returns:

value of the attribute

setExternalReference

public void setExternalReference(ExternalReference externalReference)

Set method for externalReference

Specified by:

setExternalReference in interface HasExternalReference

getExternalReference

public ExternalReference getExternalReference()

Get method for externalReference

Specified by:

getExternalReference in interface HasExternalReference

Returns:

value of the attribute

setAnnotations

public void setAnnotations(HasAnnotations.Annotations_list annotations)

Set method for annotations

Specified by:

setAnnotations in interface HasAnnotations

getAnnotations

public HasAnnotations.Annotations_list getAnnotations()

Get method for annotations

Specified by:

getAnnotations in interface HasAnnotations

Returns:

value of the attribute

addToAnnotations

public void addToAnnotations(OntologyEntry ontologyEntry)

Method to add OntologyEntry to Annotations_list

Specified by:

addToAnnotations in interface HasAnnotations

addToAnnotations

public void addToAnnotations(int position,
                             OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to Annotations_list

Specified by:

addToAnnotations in interface HasAnnotations

getFromAnnotations

public OntologyEntry getFromAnnotations(int position)

Method to get OntologyEntry from Annotations_list

Specified by:

getFromAnnotations in interface HasAnnotations

removeElementAtFromAnnotations

public void removeElementAtFromAnnotations(int position)

Method to remove by position from Annotations_list

Specified by:

removeElementAtFromAnnotations in interface HasAnnotations

removeFromAnnotations

public void removeFromAnnotations(OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from Annotations_list

Specified by:

removeFromAnnotations in interface HasAnnotations

setDatabaseReferences

public void setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list databaseReferences)

Set method for databaseReferences

Specified by:

setDatabaseReferences in interface HasDatabaseReferences

getDatabaseReferences

public HasDatabaseReferences.DatabaseReferences_list getDatabaseReferences()

Get method for databaseReferences

Specified by:

getDatabaseReferences in interface HasDatabaseReferences

Returns:

value of the attribute

addToDatabaseReferences

public void addToDatabaseReferences(DatabaseEntry databaseEntry)

Method to add DatabaseEntry to DatabaseReferences_list

Specified by:

addToDatabaseReferences in interface HasDatabaseReferences

addToDatabaseReferences

public void addToDatabaseReferences(int position,
                                    DatabaseEntry databaseEntry)

Method to add DatabaseEntry at position to DatabaseReferences_list

Specified by:

addToDatabaseReferences in interface HasDatabaseReferences

getFromDatabaseReferences

public DatabaseEntry getFromDatabaseReferences(int position)

Method to get DatabaseEntry from DatabaseReferences_list

Specified by:

getFromDatabaseReferences in interface HasDatabaseReferences

removeElementAtFromDatabaseReferences

public void removeElementAtFromDatabaseReferences(int position)

Method to remove by position from DatabaseReferences_list

Specified by:

removeElementAtFromDatabaseReferences in interface HasDatabaseReferences

removeFromDatabaseReferences

public void removeFromDatabaseReferences(DatabaseEntry databaseEntry)

Method to remove first DatabaseEntry from DatabaseReferences_list

Specified by:

removeFromDatabaseReferences in interface HasDatabaseReferences

setBibliographicReferences

public void setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list bibliographicReferences)

Set method for bibliographicReferences

Specified by:

setBibliographicReferences in interface HasBibliographicReferences

getBibliographicReferences

public HasBibliographicReferences.BibliographicReferences_list getBibliographicReferences()

Get method for bibliographicReferences

Specified by:

getBibliographicReferences in interface HasBibliographicReferences

Returns:

value of the attribute

addToBibliographicReferences

public void addToBibliographicReferences(BibliographicReference bibliographicReference)

Method to add BibliographicReference to BibliographicReferences_list

Specified by:

addToBibliographicReferences in interface HasBibliographicReferences

addToBibliographicReferences

public void addToBibliographicReferences(int position,
                                         BibliographicReference bibliographicReference)

Method to add BibliographicReference at position to BibliographicReferences_list

Specified by:

addToBibliographicReferences in interface HasBibliographicReferences

getFromBibliographicReferences

public BibliographicReference getFromBibliographicReferences(int position)

Method to get BibliographicReference from BibliographicReferences_list

Specified by:

getFromBibliographicReferences in interface HasBibliographicReferences

removeElementAtFromBibliographicReferences

public void removeElementAtFromBibliographicReferences(int position)

Method to remove by position from BibliographicReferences_list

Specified by:

removeElementAtFromBibliographicReferences in interface HasBibliographicReferences

removeFromBibliographicReferences

public void removeFromBibliographicReferences(BibliographicReference bibliographicReference)

Method to remove first BibliographicReference from BibliographicReferences_list

Specified by:

removeFromBibliographicReferences in interface HasBibliographicReferences