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org.biomage.Common
Class Describable  view Describable download Describable.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.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

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.


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.


auditTrail

private org.biomage.Interface.HasAuditTrail.AuditTrail_list auditTrail
A list of Audit instances that track changes to the instance of Describable.


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.


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

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

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

setSecurity

public void setSecurity(org.biomage.AuditAndSecurity.Security security)
Set method for security

Specified by:
setSecurity in interface org.biomage.Interface.HasSecurity

getSecurity

public org.biomage.AuditAndSecurity.Security getSecurity()
Get method for security

Specified by:
getSecurity in interface org.biomage.Interface.HasSecurity

setAuditTrail

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

Specified by:
setAuditTrail in interface org.biomage.Interface.HasAuditTrail

getAuditTrail

public org.biomage.Interface.HasAuditTrail.AuditTrail_list getAuditTrail()
Get method for auditTrail

Specified by:
getAuditTrail in interface org.biomage.Interface.HasAuditTrail

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

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

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

removeElementAtFromAuditTrail

public void removeElementAtFromAuditTrail(int position)
Method to remove by position from AuditTrail_list

Specified by:
removeElementAtFromAuditTrail in interface org.biomage.Interface.HasAuditTrail

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

setDescriptions

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

Specified by:
setDescriptions in interface org.biomage.Interface.HasDescriptions

getDescriptions

public org.biomage.Interface.HasDescriptions.Descriptions_list getDescriptions()
Get method for descriptions

Specified by:
getDescriptions in interface org.biomage.Interface.HasDescriptions

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

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

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

removeElementAtFromDescriptions

public void removeElementAtFromDescriptions(int position)
Method to remove by position from Descriptions_list

Specified by:
removeElementAtFromDescriptions in interface org.biomage.Interface.HasDescriptions

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