org.biomage.Common
Class Describable

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasPropertySets, HasSecurity
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/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  Security security
          Information on the security for the instance of the class.
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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, 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

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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Extendable

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
Throws:
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
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 Extendable
Throws:
java.io.IOException

getModelClassName

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

setDescriptions

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

Specified by:
setDescriptions in interface HasDescriptions
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

getSecurity

public Security getSecurity()
Get method for security

Specified by:
getSecurity in interface HasSecurity
Returns:
value of the attribute