org.biomage.Description
Class Description

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Description.Description
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAnnotations, HasAuditTrail, HasBibliographicReferences, HasDatabaseReferences, HasDescriptions, HasExternalReference, HasPropertySets, HasSecurity

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/interfaces inherited from interface org.biomage.Interface.HasDatabaseReferences
HasDatabaseReferences.DatabaseReferences_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBibliographicReferences
HasBibliographicReferences.BibliographicReferences_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAnnotations
HasAnnotations.Annotations_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List annotations
          Allows specification of ontology entries related to the instance being described.
protected  java.util.List bibliographicReferences
          References to existing literature.
protected  java.util.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
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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 getModelClassName()
           
 java.lang.String getText()
          Get method for text
 java.lang.String getURI()
          Get method for URI
 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 setURI(java.lang.String URI)
          Set method for URI
 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, setAttributes, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

externalReference

protected ExternalReference externalReference
Specifies where the described instance was originally obtained from.


annotations

protected java.util.List annotations
Allows specification of ontology entries related to the instance being described.


databaseReferences

protected java.util.List databaseReferences
References to entries in databases.


bibliographicReferences

protected java.util.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

Parameters:
atts: - the attribute list.
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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

setText

public void setText(java.lang.String text)
Set method for text

Parameters:
value - to set

getText

public java.lang.String getText()
Get method for text

Returns:
value of the attribute

setURI

public void setURI(java.lang.String URI)
Set method for URI

Parameters:
value - to set

getURI

public java.lang.String getURI()
Get method for URI

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Describable

setExternalReference

public void setExternalReference(ExternalReference externalReference)
Set method for externalReference

Specified by:
setExternalReference in interface HasExternalReference
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

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