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

java.lang.Object
  extended byorg.biomage.BioEvent.BioEvent_package
All Implemented Interfaces:
java.io.Serializable

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.


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).


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.


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.


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.


setBioEvent_list

public void setBioEvent_list(BioEvent_package.BioEvent_list bioEvent_list)
Set method for bioEvent_list


getBioEvent_list

public BioEvent_package.BioEvent_list getBioEvent_list()
Get method for bioEvent_list


addToBioEvent_list

public void addToBioEvent_list(BioEvent bioEvent)
Method to add BioEvent to BioEvent_list


addToBioEvent_list

public void addToBioEvent_list(int position,
                               BioEvent bioEvent)
Method to add BioEvent at position to BioEvent_list


getFromBioEvent_list

public BioEvent getFromBioEvent_list(int position)
Method to get BioEvent from BioEvent_list


removeElementAtFromBioEvent_list

public void removeElementAtFromBioEvent_list(int position)
Method to remove by position from BioEvent_list


removeFromBioEvent_list

public void removeFromBioEvent_list(BioEvent bioEvent)
Method to remove first BioEvent from BioEvent_list


setMap_list

public void setMap_list(BioEvent_package.Map_list map_list)
Set method for map_list


getMap_list

public BioEvent_package.Map_list getMap_list()
Get method for map_list


addToMap_list

public void addToMap_list(Map map)
Method to add Map to Map_list


addToMap_list

public void addToMap_list(int position,
                          Map map)
Method to add Map at position to Map_list


getFromMap_list

public Map getFromMap_list(int position)
Method to get Map from Map_list


removeElementAtFromMap_list

public void removeElementAtFromMap_list(int position)
Method to remove by position from Map_list


removeFromMap_list

public void removeFromMap_list(Map map)
Method to remove first Map from Map_list