Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep

org.biomage.Protocol
Class Protocol_package  view Protocol_package download Protocol_package.java

java.lang.Object
  extended byorg.biomage.Protocol.Protocol_package
All Implemented Interfaces:
java.io.Serializable

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.


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.


software_list

public Protocol_package.Software_list software_list
Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...


hardware_list

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


parameterizable_list

public Protocol_package.Parameterizable_list parameterizable_list
The Parameterizable interface encapsulates the association of Parameters with ParameterValues.


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.


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.


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.


setProtocol_list

public void setProtocol_list(Protocol_package.Protocol_list protocol_list)
Set method for protocol_list


getProtocol_list

public Protocol_package.Protocol_list getProtocol_list()
Get method for protocol_list


addToProtocol_list

public void addToProtocol_list(Protocol protocol)
Method to add Protocol to Protocol_list


addToProtocol_list

public void addToProtocol_list(int position,
                               Protocol protocol)
Method to add Protocol at position to Protocol_list


getFromProtocol_list

public Protocol getFromProtocol_list(int position)
Method to get Protocol from Protocol_list


removeElementAtFromProtocol_list

public void removeElementAtFromProtocol_list(int position)
Method to remove by position from Protocol_list


removeFromProtocol_list

public void removeFromProtocol_list(Protocol protocol)
Method to remove first Protocol from Protocol_list


setSoftware_list

public void setSoftware_list(Protocol_package.Software_list software_list)
Set method for software_list


getSoftware_list

public Protocol_package.Software_list getSoftware_list()
Get method for software_list


addToSoftware_list

public void addToSoftware_list(Software software)
Method to add Software to Software_list


addToSoftware_list

public void addToSoftware_list(int position,
                               Software software)
Method to add Software at position to Software_list


getFromSoftware_list

public Software getFromSoftware_list(int position)
Method to get Software from Software_list


removeElementAtFromSoftware_list

public void removeElementAtFromSoftware_list(int position)
Method to remove by position from Software_list


removeFromSoftware_list

public void removeFromSoftware_list(Software software)
Method to remove first Software from Software_list


setHardware_list

public void setHardware_list(Protocol_package.Hardware_list hardware_list)
Set method for hardware_list


getHardware_list

public Protocol_package.Hardware_list getHardware_list()
Get method for hardware_list


addToHardware_list

public void addToHardware_list(Hardware hardware)
Method to add Hardware to Hardware_list


addToHardware_list

public void addToHardware_list(int position,
                               Hardware hardware)
Method to add Hardware at position to Hardware_list


getFromHardware_list

public Hardware getFromHardware_list(int position)
Method to get Hardware from Hardware_list


removeElementAtFromHardware_list

public void removeElementAtFromHardware_list(int position)
Method to remove by position from Hardware_list


removeFromHardware_list

public void removeFromHardware_list(Hardware hardware)
Method to remove first Hardware from Hardware_list


setParameterizable_list

public void setParameterizable_list(Protocol_package.Parameterizable_list parameterizable_list)
Set method for parameterizable_list


getParameterizable_list

public Protocol_package.Parameterizable_list getParameterizable_list()
Get method for parameterizable_list


addToParameterizable_list

public void addToParameterizable_list(Parameterizable parameterizable)
Method to add Parameterizable to Parameterizable_list


addToParameterizable_list

public void addToParameterizable_list(int position,
                                      Parameterizable parameterizable)
Method to add Parameterizable at position to Parameterizable_list


getFromParameterizable_list

public Parameterizable getFromParameterizable_list(int position)
Method to get Parameterizable from Parameterizable_list


removeElementAtFromParameterizable_list

public void removeElementAtFromParameterizable_list(int position)
Method to remove by position from Parameterizable_list


removeFromParameterizable_list

public void removeFromParameterizable_list(Parameterizable parameterizable)
Method to remove first Parameterizable from Parameterizable_list


setParameterizableApplication_list

public void setParameterizableApplication_list(Protocol_package.ParameterizableApplication_list parameterizableApplication_list)
Set method for parameterizableApplication_list


getParameterizableApplication_list

public Protocol_package.ParameterizableApplication_list getParameterizableApplication_list()
Get method for parameterizableApplication_list


addToParameterizableApplication_list

public void addToParameterizableApplication_list(ParameterizableApplication parameterizableApplication)
Method to add ParameterizableApplication to ParameterizableApplication_list


addToParameterizableApplication_list

public void addToParameterizableApplication_list(int position,
                                                 ParameterizableApplication parameterizableApplication)
Method to add ParameterizableApplication at position to ParameterizableApplication_list


getFromParameterizableApplication_list

public ParameterizableApplication getFromParameterizableApplication_list(int position)
Method to get ParameterizableApplication from ParameterizableApplication_list


removeElementAtFromParameterizableApplication_list

public void removeElementAtFromParameterizableApplication_list(int position)
Method to remove by position from ParameterizableApplication_list


removeFromParameterizableApplication_list

public void removeFromParameterizableApplication_list(ParameterizableApplication parameterizableApplication)
Method to remove first ParameterizableApplication from ParameterizableApplication_list