org.biomage.Common
Class Describable

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

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasPropertySets, HasSecurity, java.io.Serializable

Direct Known Subclasses:

Audit, BibliographicReference, Description, ExperimentDesign, Fiducial, Identifiable, ManufactureLIMS, Node, NodeContents, ParameterizableApplication, SeqFeature

public abstract class Describable

extends Extendable

implements java.io.Serializable, HasSecurity, HasAuditTrail, HasDescriptions

Abstract class that allows subclasses to inherit the association to Description, for detailed annotations such as Ontology entries and Database references, the association to Audit, for tracking changes, and the association to Security for indicating permissions.

See Also:

Serialized Form

Nested Class Summary

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 HasAuditTrail.AuditTrail_list	auditTrail A list of Audit instances that track changes to the instance of Describable.
protected HasDescriptions.Descriptions_list	descriptions Free hand text descriptions.
protected Security	security Information on the security for the instance of the class.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Describable()
Default constructor.

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

Method Summary

void	addToAuditTrail(Audit audit) Method to add Audit to AuditTrail_list
void	addToAuditTrail(int position, Audit audit) Method to add Audit at position to AuditTrail_list
void	addToDescriptions(Description description) Method to add Description to Descriptions_list
void	addToDescriptions(int position, Description description) Method to add Description at position to Descriptions_list
HasAuditTrail.AuditTrail_list	getAuditTrail() Get method for auditTrail
HasDescriptions.Descriptions_list	getDescriptions() Get method for descriptions
Audit	getFromAuditTrail(int position) Method to get Audit from AuditTrail_list
Description	getFromDescriptions(int position) Method to get Description from Descriptions_list
Security	getSecurity() Get method for security
void	removeElementAtFromAuditTrail(int position) Method to remove by position from AuditTrail_list
void	removeElementAtFromDescriptions(int position) Method to remove by position from Descriptions_list
void	removeFromAuditTrail(Audit audit) Method to remove first Audit from AuditTrail_list
void	removeFromDescriptions(Description description) Method to remove first Description from Descriptions_list
void	setAuditTrail(HasAuditTrail.AuditTrail_list auditTrail) Set method for auditTrail
void	setDescriptions(HasDescriptions.Descriptions_list descriptions) Set method for descriptions
void	setSecurity(Security security) Set method for security
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

descriptions

protected HasDescriptions.Descriptions_list descriptions

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

auditTrail

protected HasAuditTrail.AuditTrail_list auditTrail

A list of Audit instances that track changes to the instance of Describable.

security

protected Security security

Information on the security for the instance of the class.

Constructor Detail

Describable

public Describable()

Default constructor.

Describable

public Describable(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

setDescriptions

public void setDescriptions(HasDescriptions.Descriptions_list descriptions)

Set method for descriptions

Specified by:

setDescriptions in interface HasDescriptions

getDescriptions

public HasDescriptions.Descriptions_list getDescriptions()

Get method for descriptions

Specified by:

getDescriptions in interface HasDescriptions

Returns:

value of the attribute

addToDescriptions

public void addToDescriptions(Description description)

Method to add Description to Descriptions_list

Specified by:

addToDescriptions in interface HasDescriptions

addToDescriptions

public void addToDescriptions(int position,
                              Description description)

Method to add Description at position to Descriptions_list

Specified by:

addToDescriptions in interface HasDescriptions

getFromDescriptions

public Description getFromDescriptions(int position)

Method to get Description from Descriptions_list

Specified by:

getFromDescriptions in interface HasDescriptions

removeElementAtFromDescriptions

public void removeElementAtFromDescriptions(int position)

Method to remove by position from Descriptions_list

Specified by:

removeElementAtFromDescriptions in interface HasDescriptions

removeFromDescriptions

public void removeFromDescriptions(Description description)

Method to remove first Description from Descriptions_list

Specified by:

removeFromDescriptions in interface HasDescriptions

setAuditTrail

public void setAuditTrail(HasAuditTrail.AuditTrail_list auditTrail)

Set method for auditTrail

Specified by:

setAuditTrail in interface HasAuditTrail

getAuditTrail

public HasAuditTrail.AuditTrail_list getAuditTrail()

Get method for auditTrail

Specified by:

getAuditTrail in interface HasAuditTrail

Returns:

value of the attribute

addToAuditTrail

public void addToAuditTrail(Audit audit)

Method to add Audit to AuditTrail_list

Specified by:

addToAuditTrail in interface HasAuditTrail

addToAuditTrail

public void addToAuditTrail(int position,
                            Audit audit)

Method to add Audit at position to AuditTrail_list

Specified by:

addToAuditTrail in interface HasAuditTrail

getFromAuditTrail

public Audit getFromAuditTrail(int position)

Method to get Audit from AuditTrail_list

Specified by:

getFromAuditTrail in interface HasAuditTrail

removeElementAtFromAuditTrail

public void removeElementAtFromAuditTrail(int position)

Method to remove by position from AuditTrail_list

Specified by:

removeElementAtFromAuditTrail in interface HasAuditTrail

removeFromAuditTrail

public void removeFromAuditTrail(Audit audit)

Method to remove first Audit from AuditTrail_list

Specified by:

removeFromAuditTrail in interface HasAuditTrail

setSecurity

public void setSecurity(Security security)

Set method for security

Specified by:

setSecurity in interface HasSecurity

getSecurity

public Security getSecurity()

Get method for security

Specified by:

getSecurity in interface HasSecurity

Returns:

value of the attribute