org.biomage.BioEvent
Class BioEvent

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioEvent.BioEvent
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasPropertySets, HasProtocolApplications, HasSecurity
Direct Known Subclasses:
BioAssayCreation, BioAssayTreatment, FeatureExtraction, Map, Transformation, Treatment

public abstract class BioEvent
extends Identifiable
implements java.io.Serializable, HasProtocolApplications

An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_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
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioEvent()
          Default constructor.
BioEvent(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToProtocolApplications(int position, ProtocolApplication protocolApplication)
          Method to add ProtocolApplication at position to ProtocolApplications_list
 void addToProtocolApplications(ProtocolApplication protocolApplication)
          Method to add ProtocolApplication to ProtocolApplications_list
 ProtocolApplication getFromProtocolApplications(int position)
          Method to get ProtocolApplication from ProtocolApplications_list
 java.lang.String getModelClassName()
           
 HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
          Get method for protocolApplications
 void removeElementAtFromProtocolApplications(int position)
          Method to remove by position from ProtocolApplications_list
 void removeFromProtocolApplications(ProtocolApplication protocolApplication)
          Method to remove first ProtocolApplication from ProtocolApplications_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
          Set method for protocolApplications
 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.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, 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
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

BioEvent

public BioEvent()
Default constructor.


BioEvent

public BioEvent(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 Identifiable

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 Identifiable
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 Identifiable
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 Identifiable
Throws:
java.io.IOException

getModelClassName

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

setProtocolApplications

public void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
Set method for protocolApplications

Specified by:
setProtocolApplications in interface HasProtocolApplications
Parameters:
value - to set

getProtocolApplications

public HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
Get method for protocolApplications

Specified by:
getProtocolApplications in interface HasProtocolApplications
Returns:
value of the attribute

addToProtocolApplications

public void addToProtocolApplications(ProtocolApplication protocolApplication)
Method to add ProtocolApplication to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(int position,
                                      ProtocolApplication protocolApplication)
Method to add ProtocolApplication at position to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface HasProtocolApplications

getFromProtocolApplications

public ProtocolApplication getFromProtocolApplications(int position)
Method to get ProtocolApplication from ProtocolApplications_list

Specified by:
getFromProtocolApplications in interface HasProtocolApplications

removeElementAtFromProtocolApplications

public void removeElementAtFromProtocolApplications(int position)
Method to remove by position from ProtocolApplications_list

Specified by:
removeElementAtFromProtocolApplications in interface HasProtocolApplications

removeFromProtocolApplications

public void removeFromProtocolApplications(ProtocolApplication protocolApplication)
Method to remove first ProtocolApplication from ProtocolApplications_list

Specified by:
removeFromProtocolApplications in interface HasProtocolApplications