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org.biomage.Protocol
Class Protocol_package  

java.lang.Object
  org.biomage.Protocol.Protocol_package

All Implemented Interfaces:

java.io.Serializable

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public class Protocol_package

extends java.lang.Object

implements java.io.Serializable

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. The ProtocolApplication provides values for the replaceable parameters of the Protocol and, through the Description association of Describable, any variation from the Protocol.

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Nested Class Summary
class	Protocol_package.Hardware_list           Inner list class for holding multiple entries for attribute hardware_list.
class	Protocol_package.Parameterizable_list           Inner list class for holding multiple entries for attribute parameterizable_list.
class	Protocol_package.ParameterizableApplication_list           Inner list class for holding multiple entries for attribute parameterizableApplication_list.
class	Protocol_package.Protocol_list           Inner list class for holding multiple entries for attribute protocol_list.
class	Protocol_package.Software_list           Inner list class for holding multiple entries for attribute software_list.

 

Field Summary
Protocol_package.Hardware_list	hardware_list           Hardware represents the hardware used.
Protocol_package.Parameterizable_list	parameterizable_list           The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
Protocol_package.ParameterizableApplication_list	parameterizableApplication_list           The interface that is the use of a Parameterizable class.
Protocol_package.Protocol_list	protocol_list           A Protocol is a parameterizable description of a method.
Protocol_package.Software_list	software_list           Software represents the software used.

 

Constructor Summary

Protocol_package()           Default constructor.

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

 

Method Summary
void	addToHardware_list(Hardware hardware)           Method to add Hardware to Hardware_list
void	addToHardware_list(int position, Hardware hardware)           Method to add Hardware at position to Hardware_list
void	addToParameterizable_list(int position, Parameterizable parameterizable)           Method to add Parameterizable at position to Parameterizable_list
void	addToParameterizable_list(Parameterizable parameterizable)           Method to add Parameterizable to Parameterizable_list
void	addToParameterizableApplication_list(int position, ParameterizableApplication parameterizableApplication)           Method to add ParameterizableApplication at position to ParameterizableApplication_list
void	addToParameterizableApplication_list(ParameterizableApplication parameterizableApplication)           Method to add ParameterizableApplication to ParameterizableApplication_list
void	addToProtocol_list(int position, Protocol protocol)           Method to add Protocol at position to Protocol_list
void	addToProtocol_list(Protocol protocol)           Method to add Protocol to Protocol_list
void	addToSoftware_list(int position, Software software)           Method to add Software at position to Software_list
void	addToSoftware_list(Software software)           Method to add Software to Software_list
Hardware	getFromHardware_list(int position)           Method to get Hardware from Hardware_list
Parameterizable	getFromParameterizable_list(int position)           Method to get Parameterizable from Parameterizable_list
ParameterizableApplication	getFromParameterizableApplication_list(int position)           Method to get ParameterizableApplication from ParameterizableApplication_list
Protocol	getFromProtocol_list(int position)           Method to get Protocol from Protocol_list
Software	getFromSoftware_list(int position)           Method to get Software from Software_list
Protocol_package.Hardware_list	getHardware_list()           Get method for hardware_list
Protocol_package.Parameterizable_list	getParameterizable_list()           Get method for parameterizable_list
Protocol_package.ParameterizableApplication_list	getParameterizableApplication_list()           Get method for parameterizableApplication_list
Protocol_package.Protocol_list	getProtocol_list()           Get method for protocol_list
Protocol_package.Software_list	getSoftware_list()           Get method for software_list
void	removeElementAtFromHardware_list(int position)           Method to remove by position from Hardware_list
void	removeElementAtFromParameterizable_list(int position)           Method to remove by position from Parameterizable_list
void	removeElementAtFromParameterizableApplication_list(int position)           Method to remove by position from ParameterizableApplication_list
void	removeElementAtFromProtocol_list(int position)           Method to remove by position from Protocol_list
void	removeElementAtFromSoftware_list(int position)           Method to remove by position from Software_list
void	removeFromHardware_list(Hardware hardware)           Method to remove first Hardware from Hardware_list
void	removeFromParameterizable_list(Parameterizable parameterizable)           Method to remove first Parameterizable from Parameterizable_list
void	removeFromParameterizableApplication_list(ParameterizableApplication parameterizableApplication)           Method to remove first ParameterizableApplication from ParameterizableApplication_list
void	removeFromProtocol_list(Protocol protocol)           Method to remove first Protocol from Protocol_list
void	removeFromSoftware_list(Software software)           Method to remove first Software from Software_list
void	setHardware_list(Protocol_package.Hardware_list hardware_list)           Set method for hardware_list
void	setParameterizable_list(Protocol_package.Parameterizable_list parameterizable_list)           Set method for parameterizable_list
void	setParameterizableApplication_list(Protocol_package.ParameterizableApplication_list parameterizableApplication_list)           Set method for parameterizableApplication_list
void	setProtocol_list(Protocol_package.Protocol_list protocol_list)           Set method for protocol_list
void	setSoftware_list(Protocol_package.Software_list software_list)           Set method for software_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

protocol_list

public Protocol_package.Protocol_list protocol_list

A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of it's Protocol's Parameters.

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software_list

public Protocol_package.Software_list software_list

Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...

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hardware_list

public Protocol_package.Hardware_list hardware_list

Hardware represents the hardware used. Examples of Hardware include: computers, scanners, wash stations etc...

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parameterizable_list

public Protocol_package.Parameterizable_list parameterizable_list

The Parameterizable interface encapsulates the association of Parameters with ParameterValues.

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parameterizableApplication_list

public Protocol_package.ParameterizableApplication_list parameterizableApplication_list

The interface that is the use of a Parameterizable class.

Constructor Detail

Protocol_package

public Protocol_package()

Default constructor.

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Protocol_package

public Protocol_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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setProtocol_list

public void setProtocol_list(Protocol_package.Protocol_list protocol_list)

Set method for protocol_list

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getProtocol_list

public Protocol_package.Protocol_list getProtocol_list()

Get method for protocol_list

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addToProtocol_list

public void addToProtocol_list(Protocol protocol)

Method to add Protocol to Protocol_list

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addToProtocol_list

public void addToProtocol_list(int position,
                               Protocol protocol)

Method to add Protocol at position to Protocol_list

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getFromProtocol_list

public Protocol getFromProtocol_list(int position)

Method to get Protocol from Protocol_list

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removeElementAtFromProtocol_list

public void removeElementAtFromProtocol_list(int position)

Method to remove by position from Protocol_list

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removeFromProtocol_list

public void removeFromProtocol_list(Protocol protocol)

Method to remove first Protocol from Protocol_list

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setSoftware_list

public void setSoftware_list(Protocol_package.Software_list software_list)

Set method for software_list

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getSoftware_list

public Protocol_package.Software_list getSoftware_list()

Get method for software_list

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addToSoftware_list

public void addToSoftware_list(Software software)

Method to add Software to Software_list

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addToSoftware_list

public void addToSoftware_list(int position,
                               Software software)

Method to add Software at position to Software_list

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getFromSoftware_list

public Software getFromSoftware_list(int position)

Method to get Software from Software_list

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removeElementAtFromSoftware_list

public void removeElementAtFromSoftware_list(int position)

Method to remove by position from Software_list

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removeFromSoftware_list

public void removeFromSoftware_list(Software software)

Method to remove first Software from Software_list

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setHardware_list

public void setHardware_list(Protocol_package.Hardware_list hardware_list)

Set method for hardware_list

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getHardware_list

public Protocol_package.Hardware_list getHardware_list()

Get method for hardware_list

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addToHardware_list

public void addToHardware_list(Hardware hardware)

Method to add Hardware to Hardware_list

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addToHardware_list

public void addToHardware_list(int position,
                               Hardware hardware)

Method to add Hardware at position to Hardware_list

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getFromHardware_list

public Hardware getFromHardware_list(int position)

Method to get Hardware from Hardware_list

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removeElementAtFromHardware_list

public void removeElementAtFromHardware_list(int position)

Method to remove by position from Hardware_list

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removeFromHardware_list

public void removeFromHardware_list(Hardware hardware)

Method to remove first Hardware from Hardware_list

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setParameterizable_list

public void setParameterizable_list(Protocol_package.Parameterizable_list parameterizable_list)

Set method for parameterizable_list

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getParameterizable_list

public Protocol_package.Parameterizable_list getParameterizable_list()

Get method for parameterizable_list

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addToParameterizable_list

public void addToParameterizable_list(Parameterizable parameterizable)

Method to add Parameterizable to Parameterizable_list

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addToParameterizable_list

public void addToParameterizable_list(int position,
                                      Parameterizable parameterizable)

Method to add Parameterizable at position to Parameterizable_list

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getFromParameterizable_list

public Parameterizable getFromParameterizable_list(int position)

Method to get Parameterizable from Parameterizable_list

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removeElementAtFromParameterizable_list

public void removeElementAtFromParameterizable_list(int position)

Method to remove by position from Parameterizable_list

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removeFromParameterizable_list

public void removeFromParameterizable_list(Parameterizable parameterizable)

Method to remove first Parameterizable from Parameterizable_list

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setParameterizableApplication_list

public void setParameterizableApplication_list(Protocol_package.ParameterizableApplication_list parameterizableApplication_list)

Set method for parameterizableApplication_list

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getParameterizableApplication_list

public Protocol_package.ParameterizableApplication_list getParameterizableApplication_list()

Get method for parameterizableApplication_list

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addToParameterizableApplication_list

public void addToParameterizableApplication_list(ParameterizableApplication parameterizableApplication)

Method to add ParameterizableApplication to ParameterizableApplication_list

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addToParameterizableApplication_list

public void addToParameterizableApplication_list(int position,
                                                 ParameterizableApplication parameterizableApplication)

Method to add ParameterizableApplication at position to ParameterizableApplication_list

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getFromParameterizableApplication_list

public ParameterizableApplication getFromParameterizableApplication_list(int position)

Method to get ParameterizableApplication from ParameterizableApplication_list

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removeElementAtFromParameterizableApplication_list

public void removeElementAtFromParameterizableApplication_list(int position)

Method to remove by position from ParameterizableApplication_list

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removeFromParameterizableApplication_list

public void removeFromParameterizableApplication_list(ParameterizableApplication parameterizableApplication)

Method to remove first ParameterizableApplication from ParameterizableApplication_list

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

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