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org.biomage.Common
Class Describable  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

Direct Known Subclasses:

Identifiable

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public abstract class Describable

extends Extendable

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

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Nested Class Summary

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Interface.HasAuditTrail.AuditTrail_list	auditTrail           A list of Audit instances that track changes to the instance of Describable.
private  org.biomage.Interface.HasDescriptions.Descriptions_list	descriptions           Free hand text descriptions.
private  org.biomage.AuditAndSecurity.Security	security           Information on the security for the instance of the class.

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

Describable()           Default constructor.

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

 

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

security

private org.biomage.AuditAndSecurity.Security security

Information on the security for the instance of the class.

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auditTrail

private org.biomage.Interface.HasAuditTrail.AuditTrail_list auditTrail

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

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descriptions

private org.biomage.Interface.HasDescriptions.Descriptions_list descriptions

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

Constructor Detail

Describable

public Describable()

Default constructor.

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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

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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.

Overrides:

writeAttributes in class Extendable

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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.

Overrides:

writeAssociations in class Extendable

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setSecurity

public void setSecurity(org.biomage.AuditAndSecurity.Security security)

Set method for security

Specified by:

setSecurity in interface org.biomage.Interface.HasSecurity

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getSecurity

public org.biomage.AuditAndSecurity.Security getSecurity()

Get method for security

Specified by:

getSecurity in interface org.biomage.Interface.HasSecurity

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setAuditTrail

public void setAuditTrail(org.biomage.Interface.HasAuditTrail.AuditTrail_list auditTrail)

Set method for auditTrail

Specified by:

setAuditTrail in interface org.biomage.Interface.HasAuditTrail

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getAuditTrail

public org.biomage.Interface.HasAuditTrail.AuditTrail_list getAuditTrail()

Get method for auditTrail

Specified by:

getAuditTrail in interface org.biomage.Interface.HasAuditTrail

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addToAuditTrail

public void addToAuditTrail(org.biomage.AuditAndSecurity.Audit audit)

Method to add Audit to AuditTrail_list

Specified by:

addToAuditTrail in interface org.biomage.Interface.HasAuditTrail

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addToAuditTrail

public void addToAuditTrail(int position,
                            org.biomage.AuditAndSecurity.Audit audit)

Method to add Audit at position to AuditTrail_list

Specified by:

addToAuditTrail in interface org.biomage.Interface.HasAuditTrail

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getFromAuditTrail

public org.biomage.AuditAndSecurity.Audit getFromAuditTrail(int position)

Method to get Audit from AuditTrail_list

Specified by:

getFromAuditTrail in interface org.biomage.Interface.HasAuditTrail

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removeElementAtFromAuditTrail

public void removeElementAtFromAuditTrail(int position)

Method to remove by position from AuditTrail_list

Specified by:

removeElementAtFromAuditTrail in interface org.biomage.Interface.HasAuditTrail

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removeFromAuditTrail

public void removeFromAuditTrail(org.biomage.AuditAndSecurity.Audit audit)

Method to remove first Audit from AuditTrail_list

Specified by:

removeFromAuditTrail in interface org.biomage.Interface.HasAuditTrail

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setDescriptions

public void setDescriptions(org.biomage.Interface.HasDescriptions.Descriptions_list descriptions)

Set method for descriptions

Specified by:

setDescriptions in interface org.biomage.Interface.HasDescriptions

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getDescriptions

public org.biomage.Interface.HasDescriptions.Descriptions_list getDescriptions()

Get method for descriptions

Specified by:

getDescriptions in interface org.biomage.Interface.HasDescriptions

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addToDescriptions

public void addToDescriptions(org.biomage.Description.Description description)

Method to add Description to Descriptions_list

Specified by:

addToDescriptions in interface org.biomage.Interface.HasDescriptions

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addToDescriptions

public void addToDescriptions(int position,
                              org.biomage.Description.Description description)

Method to add Description at position to Descriptions_list

Specified by:

addToDescriptions in interface org.biomage.Interface.HasDescriptions

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getFromDescriptions

public org.biomage.Description.Description getFromDescriptions(int position)

Method to get Description from Descriptions_list

Specified by:

getFromDescriptions in interface org.biomage.Interface.HasDescriptions

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removeElementAtFromDescriptions

public void removeElementAtFromDescriptions(int position)

Method to remove by position from Descriptions_list

Specified by:

removeElementAtFromDescriptions in interface org.biomage.Interface.HasDescriptions

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removeFromDescriptions

public void removeFromDescriptions(org.biomage.Description.Description description)

Method to remove first Description from Descriptions_list

Specified by:

removeFromDescriptions in interface org.biomage.Interface.HasDescriptions

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ Common overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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