org.biomage.BioEvent
Class BioEvent

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

All Implemented Interfaces:

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

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 inherited from class org.biomage.Interface.HasProtocolApplications

HasProtocolApplications.ProtocolApplications_list

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 HasProtocolApplications.ProtocolApplications_list

protocolApplications The applied protocols to the BioEvent.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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	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

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, 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

protocolApplications

protected HasProtocolApplications.ProtocolApplications_list protocolApplications

The applied protocols to the BioEvent.

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

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 Identifiable

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

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

java.io.IOException

setProtocolApplications

public void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)

Set method for protocolApplications

Specified by:

setProtocolApplications in interface HasProtocolApplications

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