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org.biomage.BioEvent
Class BioEvent  view BioEvent download BioEvent.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, java.io.Serializable
Direct Known Subclasses:
Map

public abstract class BioEvent
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasProtocolApplications

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list
 
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.HasProtocolApplications.ProtocolApplications_list protocolApplications
          The applied protocols to the BioEvent.
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioEvent()
          Default constructor.
BioEvent(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToProtocolApplications(int position, org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to add ProtocolApplication at position to ProtocolApplications_list
 void addToProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to add ProtocolApplication to ProtocolApplications_list
 org.biomage.Protocol.ProtocolApplication getFromProtocolApplications(int position)
          Method to get ProtocolApplication from ProtocolApplications_list
 org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
          Get method for protocolApplications
 void removeElementAtFromProtocolApplications(int position)
          Method to remove by position from ProtocolApplications_list
 void removeFromProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to remove first ProtocolApplication from ProtocolApplications_list
 void setProtocolApplications(org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list protocolApplications)
          Set method for protocolApplications
 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.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

private org.biomage.Interface.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.


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.


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.


setProtocolApplications

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

Specified by:
setProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

getProtocolApplications

public org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
Get method for protocolApplications

Specified by:
getProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to add ProtocolApplication to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(int position,
                                      org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to add ProtocolApplication at position to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

getFromProtocolApplications

public org.biomage.Protocol.ProtocolApplication getFromProtocolApplications(int position)
Method to get ProtocolApplication from ProtocolApplications_list

Specified by:
getFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

removeElementAtFromProtocolApplications

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

Specified by:
removeElementAtFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

removeFromProtocolApplications

public void removeFromProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to remove first ProtocolApplication from ProtocolApplications_list

Specified by:
removeFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications