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A

addToBioEvent_list(BioEvent) - Method in class org.biomage.BioEvent.BioEvent_package
Method to add BioEvent to BioEvent_list
addToBioEvent_list(int, BioEvent) - Method in class org.biomage.BioEvent.BioEvent_package
Method to add BioEvent at position to BioEvent_list
addToMap_list(Map) - Method in class org.biomage.BioEvent.BioEvent_package
Method to add Map to Map_list
addToMap_list(int, Map) - Method in class org.biomage.BioEvent.BioEvent_package
Method to add Map at position to Map_list
addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent
Method to add ProtocolApplication to ProtocolApplications_list
addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent
Method to add ProtocolApplication at position to ProtocolApplications_list

B

BioEvent - class org.biomage.BioEvent.BioEvent.
An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
BioEvent() - Constructor for class org.biomage.BioEvent.BioEvent
Default constructor.
BioEvent(Attributes) - Constructor for class org.biomage.BioEvent.BioEvent
Attribute constructor.
BioEvent_package - class org.biomage.BioEvent.BioEvent_package.
An abstract class representing an event that takes sources of some type to produce a target of some type.
BioEvent_package() - Constructor for class org.biomage.BioEvent.BioEvent_package
Default constructor.
BioEvent_package(Attributes) - Constructor for class org.biomage.BioEvent.BioEvent_package
Attribute constructor.
BioEvent_package.BioEvent_list - class org.biomage.BioEvent.BioEvent_package.BioEvent_list.
Inner list class for holding multiple entries for attribute bioEvent_list.
BioEvent_package.BioEvent_list() - Constructor for class org.biomage.BioEvent.BioEvent_package.BioEvent_list
 
BioEvent_package.Map_list - class org.biomage.BioEvent.BioEvent_package.Map_list.
Inner list class for holding multiple entries for attribute map_list.
BioEvent_package.Map_list() - Constructor for class org.biomage.BioEvent.BioEvent_package.Map_list
 
bioEvent_list - Variable in class org.biomage.BioEvent.BioEvent_package
An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).

G

getBioEvent_list() - Method in class org.biomage.BioEvent.BioEvent_package
Get method for bioEvent_list
getFromBioEvent_list(int) - Method in class org.biomage.BioEvent.BioEvent_package
Method to get BioEvent from BioEvent_list
getFromMap_list(int) - Method in class org.biomage.BioEvent.BioEvent_package
Method to get Map from Map_list
getFromProtocolApplications(int) - Method in class org.biomage.BioEvent.BioEvent
Method to get ProtocolApplication from ProtocolApplications_list
getMap_list() - Method in class org.biomage.BioEvent.BioEvent_package
Get method for map_list
getProtocolApplications() - Method in class org.biomage.BioEvent.BioEvent
Get method for protocolApplications

M

Map - class org.biomage.BioEvent.Map.
A Map is the description of how sources are transformed into a target.
Map() - Constructor for class org.biomage.BioEvent.Map
Default constructor.
Map(Attributes) - Constructor for class org.biomage.BioEvent.Map
Attribute constructor.
map_list - Variable in class org.biomage.BioEvent.BioEvent_package
A Map is the description of how sources are transformed into a target.

O

org.biomage.BioEvent - package org.biomage.BioEvent
 

P

protocolApplications - Variable in class org.biomage.BioEvent.BioEvent
The applied protocols to the BioEvent.

R

removeElementAtFromBioEvent_list(int) - Method in class org.biomage.BioEvent.BioEvent_package
Method to remove by position from BioEvent_list
removeElementAtFromMap_list(int) - Method in class org.biomage.BioEvent.BioEvent_package
Method to remove by position from Map_list
removeElementAtFromProtocolApplications(int) - Method in class org.biomage.BioEvent.BioEvent
Method to remove by position from ProtocolApplications_list
removeFromBioEvent_list(BioEvent) - Method in class org.biomage.BioEvent.BioEvent_package
Method to remove first BioEvent from BioEvent_list
removeFromMap_list(Map) - Method in class org.biomage.BioEvent.BioEvent_package
Method to remove first Map from Map_list
removeFromProtocolApplications(ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent
Method to remove first ProtocolApplication from ProtocolApplications_list

S

setBioEvent_list(BioEvent_package.BioEvent_list) - Method in class org.biomage.BioEvent.BioEvent_package
Set method for bioEvent_list
setMap_list(BioEvent_package.Map_list) - Method in class org.biomage.BioEvent.BioEvent_package
Set method for map_list
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.BioEvent.BioEvent
Set method for protocolApplications

W

writeAssociations(Writer) - Method in class org.biomage.BioEvent.BioEvent
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.BioEvent.BioEvent_package
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.BioEvent.Map
writeAssociations
writeAttributes(Writer) - Method in class org.biomage.BioEvent.BioEvent
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.BioEvent.BioEvent_package
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.BioEvent.Map
writeAttributes
writeMAGEML(Writer) - Method in class org.biomage.BioEvent.BioEvent
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.BioEvent.BioEvent_package
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.BioEvent.Map
writeMAGEML

A B G M O P R S W