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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:

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

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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).

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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.

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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.

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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.

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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.

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setProtocolApplications

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

Set method for protocolApplications

Specified by:

setProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

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getProtocolApplications

public org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list getProtocolApplications()

Get method for protocolApplications

Specified by:

getProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

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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

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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

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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

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removeElementAtFromProtocolApplications

public void removeElementAtFromProtocolApplications(int position)

Method to remove by position from ProtocolApplications_list

Specified by:

removeElementAtFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

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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

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioEvent overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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