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A
- activityDate - Variable in class org.biomage.Protocol.ProtocolApplication
- When the protocol was applied.
- addToHardwareApplications(HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to add HardwareApplication to HardwareApplications_list
- addToHardwareApplications(int, HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to add HardwareApplication at position to HardwareApplications_list
- addToHardwareManufacturers(Contact) - Method in class org.biomage.Protocol.Hardware
- Method to add Contact to HardwareManufacturers_list
- addToHardwareManufacturers(int, Contact) - Method in class org.biomage.Protocol.Hardware
- Method to add Contact at position to HardwareManufacturers_list
- addToHardware_list(Hardware) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Hardware to Hardware_list
- addToHardware_list(int, Hardware) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Hardware at position to Hardware_list
- addToHardwares(Hardware) - Method in class org.biomage.Protocol.Protocol
- Method to add Hardware to Hardwares_list
- addToHardwares(int, Hardware) - Method in class org.biomage.Protocol.Protocol
- Method to add Hardware at position to Hardwares_list
- addToParameterTypes(Parameter) - Method in class org.biomage.Protocol.Parameterizable
- Method to add Parameter to ParameterTypes_list
- addToParameterTypes(int, Parameter) - Method in class org.biomage.Protocol.Parameterizable
- Method to add Parameter at position to ParameterTypes_list
- addToParameterValues(ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication
- Method to add ParameterValue to ParameterValues_list
- addToParameterValues(int, ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication
- Method to add ParameterValue at position to ParameterValues_list
- addToParameterizableApplication_list(ParameterizableApplication) - Method in class org.biomage.Protocol.Protocol_package
- Method to add ParameterizableApplication to ParameterizableApplication_list
- addToParameterizableApplication_list(int, ParameterizableApplication) - Method in class org.biomage.Protocol.Protocol_package
- Method to add ParameterizableApplication at position to ParameterizableApplication_list
- addToParameterizable_list(Parameterizable) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Parameterizable to Parameterizable_list
- addToParameterizable_list(int, Parameterizable) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Parameterizable at position to Parameterizable_list
- addToPerformers(Person) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to add Person to Performers_list
- addToPerformers(int, Person) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to add Person at position to Performers_list
- addToProtocol_list(Protocol) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Protocol to Protocol_list
- addToProtocol_list(int, Protocol) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Protocol at position to Protocol_list
- addToSoftwareApplications(SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to add SoftwareApplication to SoftwareApplications_list
- addToSoftwareApplications(int, SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to add SoftwareApplication at position to SoftwareApplications_list
- addToSoftwareManufacturers(Contact) - Method in class org.biomage.Protocol.Software
- Method to add Contact to SoftwareManufacturers_list
- addToSoftwareManufacturers(int, Contact) - Method in class org.biomage.Protocol.Software
- Method to add Contact at position to SoftwareManufacturers_list
- addToSoftware_list(Software) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Software to Software_list
- addToSoftware_list(int, Software) - Method in class org.biomage.Protocol.Protocol_package
- Method to add Software at position to Software_list
- addToSoftwares(Software) - Method in class org.biomage.Protocol.Hardware
- Method to add Software to Softwares_list
- addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Hardware
- Method to add Software at position to Softwares_list
- addToSoftwares(Software) - Method in class org.biomage.Protocol.Protocol
- Method to add Software to Softwares_list
- addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Protocol
- Method to add Software at position to Softwares_list
- addToSoftwares(Software) - Method in class org.biomage.Protocol.Software
- Method to add Software to Softwares_list
- addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Software
- Method to add Software at position to Softwares_list
D
- dataType - Variable in class org.biomage.Protocol.Parameter
- The type of data generated by the parameter i.e.
G
- getActivityDate() - Method in class org.biomage.Protocol.ProtocolApplication
- Get method for activityDate
- getDataType() - Method in class org.biomage.Protocol.Parameter
- Get method for dataType
- getFromHardwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to get HardwareApplication from HardwareApplications_list
- getFromHardwareManufacturers(int) - Method in class org.biomage.Protocol.Hardware
- Method to get Contact from HardwareManufacturers_list
- getFromHardware_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to get Hardware from Hardware_list
- getFromHardwares(int) - Method in class org.biomage.Protocol.Protocol
- Method to get Hardware from Hardwares_list
- getFromParameterTypes(int) - Method in class org.biomage.Protocol.Parameterizable
- Method to get Parameter from ParameterTypes_list
- getFromParameterValues(int) - Method in class org.biomage.Protocol.ParameterizableApplication
- Method to get ParameterValue from ParameterValues_list
- getFromParameterizableApplication_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to get ParameterizableApplication from ParameterizableApplication_list
- getFromParameterizable_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to get Parameterizable from Parameterizable_list
- getFromPerformers(int) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to get Person from Performers_list
- getFromProtocol_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to get Protocol from Protocol_list
- getFromSoftwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to get SoftwareApplication from SoftwareApplications_list
- getFromSoftwareManufacturers(int) - Method in class org.biomage.Protocol.Software
- Method to get Contact from SoftwareManufacturers_list
- getFromSoftware_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to get Software from Software_list
- getFromSoftwares(int) - Method in class org.biomage.Protocol.Hardware
- Method to get Software from Softwares_list
- getFromSoftwares(int) - Method in class org.biomage.Protocol.Protocol
- Method to get Software from Softwares_list
- getFromSoftwares(int) - Method in class org.biomage.Protocol.Software
- Method to get Software from Softwares_list
- getHardware() - Method in class org.biomage.Protocol.HardwareApplication
- Get method for hardware
- getHardware() - Method in class org.biomage.Protocol.Software
- Get method for hardware
- getHardwareApplications() - Method in class org.biomage.Protocol.ProtocolApplication
- Get method for hardwareApplications
- getHardwareManufacturers() - Method in class org.biomage.Protocol.Hardware
- Get method for hardwareManufacturers
- getHardware_list() - Method in class org.biomage.Protocol.Protocol_package
- Get method for hardware_list
- getHardwares() - Method in class org.biomage.Protocol.Protocol
- Get method for hardwares
- getMake() - Method in class org.biomage.Protocol.Hardware
- Get method for make
- getModel() - Method in class org.biomage.Protocol.Hardware
- Get method for model
- getParameterType() - Method in class org.biomage.Protocol.ParameterValue
- Get method for parameterType
- getParameterTypes() - Method in class org.biomage.Protocol.Parameterizable
- Get method for parameterTypes
- getParameterValues() - Method in class org.biomage.Protocol.ParameterizableApplication
- Get method for parameterValues
- getParameterizableApplication_list() - Method in class org.biomage.Protocol.Protocol_package
- Get method for parameterizableApplication_list
- getParameterizable_list() - Method in class org.biomage.Protocol.Protocol_package
- Get method for parameterizable_list
- getPerformers() - Method in class org.biomage.Protocol.ProtocolApplication
- Get method for performers
- getProtocol() - Method in class org.biomage.Protocol.ProtocolApplication
- Get method for protocol
- getProtocol_list() - Method in class org.biomage.Protocol.Protocol_package
- Get method for protocol_list
- getReleaseDate() - Method in class org.biomage.Protocol.SoftwareApplication
- Get method for releaseDate
- getSerialNumber() - Method in class org.biomage.Protocol.HardwareApplication
- Get method for serialNumber
- getSoftware() - Method in class org.biomage.Protocol.SoftwareApplication
- Get method for software
- getSoftwareApplications() - Method in class org.biomage.Protocol.ProtocolApplication
- Get method for softwareApplications
- getSoftwareManufacturers() - Method in class org.biomage.Protocol.Software
- Get method for softwareManufacturers
- getSoftware_list() - Method in class org.biomage.Protocol.Protocol_package
- Get method for software_list
- getSoftwares() - Method in class org.biomage.Protocol.Hardware
- Get method for softwares
- getSoftwares() - Method in class org.biomage.Protocol.Protocol
- Get method for softwares
- getSoftwares() - Method in class org.biomage.Protocol.Software
- Get method for softwares
- getText() - Method in class org.biomage.Protocol.Protocol
- Get method for text
- getTitle() - Method in class org.biomage.Protocol.Protocol
- Get method for title
- getType() - Method in class org.biomage.Protocol.Hardware
- Get method for type
- getType() - Method in class org.biomage.Protocol.Protocol
- Get method for type
- getType() - Method in class org.biomage.Protocol.Software
- Get method for type
- getURI() - Method in class org.biomage.Protocol.Parameterizable
- Get method for URI
- getUnit() - Method in class org.biomage.Protocol.Parameter
- Get method for unit
- getValue() - Method in class org.biomage.Protocol.ParameterValue
- Get method for value
- getVersion() - Method in class org.biomage.Protocol.SoftwareApplication
- Get method for version
H
- Hardware - class org.biomage.Protocol.Hardware.
- Hardware represents the hardware used.
- Hardware() - Constructor for class org.biomage.Protocol.Hardware
- Default constructor.
- Hardware(Attributes) - Constructor for class org.biomage.Protocol.Hardware
- Attribute constructor.
- HardwareApplication - class org.biomage.Protocol.HardwareApplication.
- The use of a piece of hardware with the requisite Parameters and ParameterValues.
- HardwareApplication() - Constructor for class org.biomage.Protocol.HardwareApplication
- Default constructor.
- HardwareApplication(Attributes) - Constructor for class org.biomage.Protocol.HardwareApplication
- Attribute constructor.
- hardware - Variable in class org.biomage.Protocol.HardwareApplication
- The underlying hardware.
- hardware - Variable in class org.biomage.Protocol.Software
- Associates Hardware and Software together.
- hardwareApplications - Variable in class org.biomage.Protocol.ProtocolApplication
- The use of hardware for the application of the protocol.
- hardwareManufacturers - Variable in class org.biomage.Protocol.Hardware
- Contact for information on the Hardware.
- hardware_list - Variable in class org.biomage.Protocol.Protocol_package
- Hardware represents the hardware used.
- hardwares - Variable in class org.biomage.Protocol.Protocol
- Hardware used by this protocol.
M
- make - Variable in class org.biomage.Protocol.Hardware
- The make of the Hardware (its manufacturer).
- model - Variable in class org.biomage.Protocol.Hardware
- The model (number) of a piece of hardware.
O
- org.biomage.Protocol - package org.biomage.Protocol
P
- Parameter - class org.biomage.Protocol.Parameter.
- A Parameter is a replaceable value in a Parameterizable class.
- Parameter() - Constructor for class org.biomage.Protocol.Parameter
- Default constructor.
- Parameter(Attributes) - Constructor for class org.biomage.Protocol.Parameter
- Attribute constructor.
- ParameterValue - class org.biomage.Protocol.ParameterValue.
- The value of a Parameter.
- ParameterValue() - Constructor for class org.biomage.Protocol.ParameterValue
- Default constructor.
- ParameterValue(Attributes) - Constructor for class org.biomage.Protocol.ParameterValue
- Attribute constructor.
- Parameterizable - class org.biomage.Protocol.Parameterizable.
- The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
- Parameterizable() - Constructor for class org.biomage.Protocol.Parameterizable
- Default constructor.
- Parameterizable(Attributes) - Constructor for class org.biomage.Protocol.Parameterizable
- Attribute constructor.
- ParameterizableApplication - class org.biomage.Protocol.ParameterizableApplication.
- The interface that is the use of a Parameterizable class.
- ParameterizableApplication() - Constructor for class org.biomage.Protocol.ParameterizableApplication
- Default constructor.
- ParameterizableApplication(Attributes) - Constructor for class org.biomage.Protocol.ParameterizableApplication
- Attribute constructor.
- Protocol - class org.biomage.Protocol.Protocol.
- A Protocol is a parameterizable description of a method.
- Protocol() - Constructor for class org.biomage.Protocol.Protocol
- Default constructor.
- Protocol(Attributes) - Constructor for class org.biomage.Protocol.Protocol
- Attribute constructor.
- ProtocolApplication - class org.biomage.Protocol.ProtocolApplication.
- The use of a protocol with the requisite Parameters and ParameterValues.
- ProtocolApplication() - Constructor for class org.biomage.Protocol.ProtocolApplication
- Default constructor.
- ProtocolApplication(Attributes) - Constructor for class org.biomage.Protocol.ProtocolApplication
- Attribute constructor.
- Protocol_package - class org.biomage.Protocol.Protocol_package.
- Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol.
- Protocol_package() - Constructor for class org.biomage.Protocol.Protocol_package
- Default constructor.
- Protocol_package(Attributes) - Constructor for class org.biomage.Protocol.Protocol_package
- Attribute constructor.
- Protocol_package.Hardware_list - class org.biomage.Protocol.Protocol_package.Hardware_list.
- Inner list class for holding multiple entries for attribute hardware_list.
- Protocol_package.Hardware_list() - Constructor for class org.biomage.Protocol.Protocol_package.Hardware_list
- Protocol_package.ParameterizableApplication_list - class org.biomage.Protocol.Protocol_package.ParameterizableApplication_list.
- Inner list class for holding multiple entries for attribute parameterizableApplication_list.
- Protocol_package.ParameterizableApplication_list() - Constructor for class org.biomage.Protocol.Protocol_package.ParameterizableApplication_list
- Protocol_package.Parameterizable_list - class org.biomage.Protocol.Protocol_package.Parameterizable_list.
- Inner list class for holding multiple entries for attribute parameterizable_list.
- Protocol_package.Parameterizable_list() - Constructor for class org.biomage.Protocol.Protocol_package.Parameterizable_list
- Protocol_package.Protocol_list - class org.biomage.Protocol.Protocol_package.Protocol_list.
- Inner list class for holding multiple entries for attribute protocol_list.
- Protocol_package.Protocol_list() - Constructor for class org.biomage.Protocol.Protocol_package.Protocol_list
- Protocol_package.Software_list - class org.biomage.Protocol.Protocol_package.Software_list.
- Inner list class for holding multiple entries for attribute software_list.
- Protocol_package.Software_list() - Constructor for class org.biomage.Protocol.Protocol_package.Software_list
- parameterType - Variable in class org.biomage.Protocol.ParameterValue
- The parameter this value is for.
- parameterTypes - Variable in class org.biomage.Protocol.Parameterizable
- The description of the parameters for the Parameterizable class instance.
- parameterValues - Variable in class org.biomage.Protocol.ParameterizableApplication
- The parameter values for this Parameterizable Application.
- parameterizableApplication_list - Variable in class org.biomage.Protocol.Protocol_package
- The interface that is the use of a Parameterizable class.
- parameterizable_list - Variable in class org.biomage.Protocol.Protocol_package
- The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
- performers - Variable in class org.biomage.Protocol.ProtocolApplication
- The people who performed the protocol.
- protocol - Variable in class org.biomage.Protocol.ProtocolApplication
- The protocol that is being used.
- protocol_list - Variable in class org.biomage.Protocol.Protocol_package
- A Protocol is a parameterizable description of a method.
R
- releaseDate - Variable in class org.biomage.Protocol.SoftwareApplication
- When the software was released.
- removeElementAtFromHardwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to remove by position from HardwareApplications_list
- removeElementAtFromHardwareManufacturers(int) - Method in class org.biomage.Protocol.Hardware
- Method to remove by position from HardwareManufacturers_list
- removeElementAtFromHardware_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove by position from Hardware_list
- removeElementAtFromHardwares(int) - Method in class org.biomage.Protocol.Protocol
- Method to remove by position from Hardwares_list
- removeElementAtFromParameterTypes(int) - Method in class org.biomage.Protocol.Parameterizable
- Method to remove by position from ParameterTypes_list
- removeElementAtFromParameterValues(int) - Method in class org.biomage.Protocol.ParameterizableApplication
- Method to remove by position from ParameterValues_list
- removeElementAtFromParameterizableApplication_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove by position from ParameterizableApplication_list
- removeElementAtFromParameterizable_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove by position from Parameterizable_list
- removeElementAtFromPerformers(int) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to remove by position from Performers_list
- removeElementAtFromProtocol_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove by position from Protocol_list
- removeElementAtFromSoftwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to remove by position from SoftwareApplications_list
- removeElementAtFromSoftwareManufacturers(int) - Method in class org.biomage.Protocol.Software
- Method to remove by position from SoftwareManufacturers_list
- removeElementAtFromSoftware_list(int) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove by position from Software_list
- removeElementAtFromSoftwares(int) - Method in class org.biomage.Protocol.Hardware
- Method to remove by position from Softwares_list
- removeElementAtFromSoftwares(int) - Method in class org.biomage.Protocol.Protocol
- Method to remove by position from Softwares_list
- removeElementAtFromSoftwares(int) - Method in class org.biomage.Protocol.Software
- Method to remove by position from Softwares_list
- removeFromHardwareApplications(HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to remove first HardwareApplication from HardwareApplications_list
- removeFromHardwareManufacturers(Contact) - Method in class org.biomage.Protocol.Hardware
- Method to remove first Contact from HardwareManufacturers_list
- removeFromHardware_list(Hardware) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove first Hardware from Hardware_list
- removeFromHardwares(Hardware) - Method in class org.biomage.Protocol.Protocol
- Method to remove first Hardware from Hardwares_list
- removeFromParameterTypes(Parameter) - Method in class org.biomage.Protocol.Parameterizable
- Method to remove first Parameter from ParameterTypes_list
- removeFromParameterValues(ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication
- Method to remove first ParameterValue from ParameterValues_list
- removeFromParameterizableApplication_list(ParameterizableApplication) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove first ParameterizableApplication from ParameterizableApplication_list
- removeFromParameterizable_list(Parameterizable) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove first Parameterizable from Parameterizable_list
- removeFromPerformers(Person) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to remove first Person from Performers_list
- removeFromProtocol_list(Protocol) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove first Protocol from Protocol_list
- removeFromSoftwareApplications(SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
- Method to remove first SoftwareApplication from SoftwareApplications_list
- removeFromSoftwareManufacturers(Contact) - Method in class org.biomage.Protocol.Software
- Method to remove first Contact from SoftwareManufacturers_list
- removeFromSoftware_list(Software) - Method in class org.biomage.Protocol.Protocol_package
- Method to remove first Software from Software_list
- removeFromSoftwares(Software) - Method in class org.biomage.Protocol.Hardware
- Method to remove first Software from Softwares_list
- removeFromSoftwares(Software) - Method in class org.biomage.Protocol.Protocol
- Method to remove first Software from Softwares_list
- removeFromSoftwares(Software) - Method in class org.biomage.Protocol.Software
- Method to remove first Software from Softwares_list
S
- Software - class org.biomage.Protocol.Software.
- Software represents the software used.
- Software() - Constructor for class org.biomage.Protocol.Software
- Default constructor.
- Software(Attributes) - Constructor for class org.biomage.Protocol.Software
- Attribute constructor.
- SoftwareApplication - class org.biomage.Protocol.SoftwareApplication.
- The use of a piece of software with the requisite Parameters and ParameterValues.
- SoftwareApplication() - Constructor for class org.biomage.Protocol.SoftwareApplication
- Default constructor.
- SoftwareApplication(Attributes) - Constructor for class org.biomage.Protocol.SoftwareApplication
- Attribute constructor.
- serialNumber - Variable in class org.biomage.Protocol.HardwareApplication
- Manufacturer's identifier for the Hardware.
- setActivityDate(String) - Method in class org.biomage.Protocol.ProtocolApplication
- Set method for activityDate
- setDataType(OntologyEntry) - Method in class org.biomage.Protocol.Parameter
- Set method for dataType
- setHardware(Hardware) - Method in class org.biomage.Protocol.HardwareApplication
- Set method for hardware
- setHardware(Hardware) - Method in class org.biomage.Protocol.Software
- Set method for hardware
- setHardwareApplications(HasHardwareApplications.HardwareApplications_list) - Method in class org.biomage.Protocol.ProtocolApplication
- Set method for hardwareApplications
- setHardwareManufacturers(HasHardwareManufacturers.HardwareManufacturers_list) - Method in class org.biomage.Protocol.Hardware
- Set method for hardwareManufacturers
- setHardware_list(Protocol_package.Hardware_list) - Method in class org.biomage.Protocol.Protocol_package
- Set method for hardware_list
- setHardwares(HasHardwares.Hardwares_list) - Method in class org.biomage.Protocol.Protocol
- Set method for hardwares
- setMake(String) - Method in class org.biomage.Protocol.Hardware
- Set method for make
- setModel(String) - Method in class org.biomage.Protocol.Hardware
- Set method for model
- setParameterType(Parameter) - Method in class org.biomage.Protocol.ParameterValue
- Set method for parameterType
- setParameterTypes(HasParameterTypes.ParameterTypes_list) - Method in class org.biomage.Protocol.Parameterizable
- Set method for parameterTypes
- setParameterValues(HasParameterValues.ParameterValues_list) - Method in class org.biomage.Protocol.ParameterizableApplication
- Set method for parameterValues
- setParameterizableApplication_list(Protocol_package.ParameterizableApplication_list) - Method in class org.biomage.Protocol.Protocol_package
- Set method for parameterizableApplication_list
- setParameterizable_list(Protocol_package.Parameterizable_list) - Method in class org.biomage.Protocol.Protocol_package
- Set method for parameterizable_list
- setPerformers(HasPerformers.Performers_list) - Method in class org.biomage.Protocol.ProtocolApplication
- Set method for performers
- setProtocol(Protocol) - Method in class org.biomage.Protocol.ProtocolApplication
- Set method for protocol
- setProtocol_list(Protocol_package.Protocol_list) - Method in class org.biomage.Protocol.Protocol_package
- Set method for protocol_list
- setReleaseDate(Date) - Method in class org.biomage.Protocol.SoftwareApplication
- Set method for releaseDate
- setSerialNumber(String) - Method in class org.biomage.Protocol.HardwareApplication
- Set method for serialNumber
- setSoftware(Software) - Method in class org.biomage.Protocol.SoftwareApplication
- Set method for software
- setSoftwareApplications(HasSoftwareApplications.SoftwareApplications_list) - Method in class org.biomage.Protocol.ProtocolApplication
- Set method for softwareApplications
- setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list) - Method in class org.biomage.Protocol.Software
- Set method for softwareManufacturers
- setSoftware_list(Protocol_package.Software_list) - Method in class org.biomage.Protocol.Protocol_package
- Set method for software_list
- setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Hardware
- Set method for softwares
- setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Protocol
- Set method for softwares
- setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Software
- Set method for softwares
- setText(String) - Method in class org.biomage.Protocol.Protocol
- Set method for text
- setTitle(String) - Method in class org.biomage.Protocol.Protocol
- Set method for title
- setType(OntologyEntry) - Method in class org.biomage.Protocol.Hardware
- Set method for type
- setType(OntologyEntry) - Method in class org.biomage.Protocol.Protocol
- Set method for type
- setType(OntologyEntry) - Method in class org.biomage.Protocol.Software
- Set method for type
- setURI(String) - Method in class org.biomage.Protocol.Parameterizable
- Set method for URI
- setUnit(Unit) - Method in class org.biomage.Protocol.Parameter
- Set method for unit
- setValue(Object) - Method in class org.biomage.Protocol.ParameterValue
- Set method for value
- setVersion(String) - Method in class org.biomage.Protocol.SoftwareApplication
- Set method for version
- software - Variable in class org.biomage.Protocol.SoftwareApplication
- The underlying software.
- softwareApplications - Variable in class org.biomage.Protocol.ProtocolApplication
- The use of software for the application of the protocol.
- softwareManufacturers - Variable in class org.biomage.Protocol.Software
- Contact for information on the software.
- software_list - Variable in class org.biomage.Protocol.Protocol_package
- Software represents the software used.
- softwares - Variable in class org.biomage.Protocol.Hardware
- Associates Hardware and Software together.
- softwares - Variable in class org.biomage.Protocol.Protocol
- Software used by this Protocol.
- softwares - Variable in class org.biomage.Protocol.Software
- Software packages this software uses, i.e.
T
- text - Variable in class org.biomage.Protocol.Protocol
- The text description of the Protocol.
- title - Variable in class org.biomage.Protocol.Protocol
- The title of the Protocol
- type - Variable in class org.biomage.Protocol.Hardware
- The type of a piece of Hardware.
- type - Variable in class org.biomage.Protocol.Protocol
- The type of a Protocol, a user should provide/use a recommended vocabulary.
- type - Variable in class org.biomage.Protocol.Software
- The type of a piece of Software.
U
- URI - Variable in class org.biomage.Protocol.Parameterizable
- Where an instantiated Parameterizable is located.
- unit - Variable in class org.biomage.Protocol.Parameter
- Unit the value is associated with
V
- value - Variable in class org.biomage.Protocol.ParameterValue
- The value of the parameter.
- version - Variable in class org.biomage.Protocol.SoftwareApplication
- The version of the software.
W
- writeAssociations(Writer) - Method in class org.biomage.Protocol.Hardware
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.HardwareApplication
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.Parameter
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.ParameterValue
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.Parameterizable
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.ParameterizableApplication
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.Protocol
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.ProtocolApplication
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.Protocol_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.Software
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Protocol.SoftwareApplication
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.Protocol.Hardware
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.HardwareApplication
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.Parameter
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.ParameterValue
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.Parameterizable
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.ParameterizableApplication
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.Protocol
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.ProtocolApplication
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.Protocol_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.Software
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Protocol.SoftwareApplication
- writeAttributes
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.Hardware
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.HardwareApplication
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.Parameter
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.ParameterValue
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.Parameterizable
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.ParameterizableApplication
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.Protocol
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.ProtocolApplication
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.Protocol_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.Software
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Protocol.SoftwareApplication
- writeMAGEML
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