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org.biomage.BioEvent
Class BioEvent_package  

java.lang.Object
  org.biomage.BioEvent.BioEvent_package

All Implemented Interfaces:

java.io.Serializable

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public class BioEvent_package

extends java.lang.Object

implements java.io.Serializable

An abstract class representing an event that takes sources of some type to produce a target of some type. Each of the realized subclasses determines the type of the sources and the target. The association to a protocol application allows specification of how the event was performed.

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Nested Class Summary
class	BioEvent_package.BioEvent_list           Inner list class for holding multiple entries for attribute bioEvent_list.
class	BioEvent_package.Map_list           Inner list class for holding multiple entries for attribute map_list.

 

Field Summary
BioEvent_package.BioEvent_list	bioEvent_list           An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
BioEvent_package.Map_list	map_list           A Map is the description of how sources are transformed into a target.

 

Constructor Summary

BioEvent_package()           Default constructor.

BioEvent_package(org.xml.sax.Attributes atts)           Attribute constructor.

 

Method Summary
void	addToBioEvent_list(BioEvent bioEvent)           Method to add BioEvent to BioEvent_list
void	addToBioEvent_list(int position, BioEvent bioEvent)           Method to add BioEvent at position to BioEvent_list
void	addToMap_list(int position, Map map)           Method to add Map at position to Map_list
void	addToMap_list(Map map)           Method to add Map to Map_list
BioEvent_package.BioEvent_list	getBioEvent_list()           Get method for bioEvent_list
BioEvent	getFromBioEvent_list(int position)           Method to get BioEvent from BioEvent_list
Map	getFromMap_list(int position)           Method to get Map from Map_list
BioEvent_package.Map_list	getMap_list()           Get method for map_list
void	removeElementAtFromBioEvent_list(int position)           Method to remove by position from BioEvent_list
void	removeElementAtFromMap_list(int position)           Method to remove by position from Map_list
void	removeFromBioEvent_list(BioEvent bioEvent)           Method to remove first BioEvent from BioEvent_list
void	removeFromMap_list(Map map)           Method to remove first Map from Map_list
void	setBioEvent_list(BioEvent_package.BioEvent_list bioEvent_list)           Set method for bioEvent_list
void	setMap_list(BioEvent_package.Map_list map_list)           Set method for map_list
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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

bioEvent_list

public BioEvent_package.BioEvent_list bioEvent_list

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

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map_list

public BioEvent_package.Map_list map_list

A Map is the description of how sources are transformed into a target. Provides an abstarct base class that separates the mapping BioEvents from the transforming.

Constructor Detail

BioEvent_package

public BioEvent_package()

Default constructor.

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BioEvent_package

public BioEvent_package(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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setBioEvent_list

public void setBioEvent_list(BioEvent_package.BioEvent_list bioEvent_list)

Set method for bioEvent_list

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getBioEvent_list

public BioEvent_package.BioEvent_list getBioEvent_list()

Get method for bioEvent_list

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addToBioEvent_list

public void addToBioEvent_list(BioEvent bioEvent)

Method to add BioEvent to BioEvent_list

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addToBioEvent_list

public void addToBioEvent_list(int position,
                               BioEvent bioEvent)

Method to add BioEvent at position to BioEvent_list

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getFromBioEvent_list

public BioEvent getFromBioEvent_list(int position)

Method to get BioEvent from BioEvent_list

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removeElementAtFromBioEvent_list

public void removeElementAtFromBioEvent_list(int position)

Method to remove by position from BioEvent_list

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removeFromBioEvent_list

public void removeFromBioEvent_list(BioEvent bioEvent)

Method to remove first BioEvent from BioEvent_list

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setMap_list

public void setMap_list(BioEvent_package.Map_list map_list)

Set method for map_list

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getMap_list

public BioEvent_package.Map_list getMap_list()

Get method for map_list

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addToMap_list

public void addToMap_list(Map map)

Method to add Map to Map_list

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addToMap_list

public void addToMap_list(int position,
                          Map map)

Method to add Map at position to Map_list

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getFromMap_list

public Map getFromMap_list(int position)

Method to get Map from Map_list

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removeElementAtFromMap_list

public void removeElementAtFromMap_list(int position)

Method to remove by position from Map_list

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removeFromMap_list

public void removeFromMap_list(Map map)

Method to remove first Map from Map_list

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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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