org.biomage.Protocol
Class Protocol_package

java.lang.Object
  extended by org.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.

See Also:
Serialized Form

Nested Class Summary
 class Protocol_package.Hardware_list
          Inner list class for holding multiple entries for attribute hardware.
 class Protocol_package.Protocol_list
          Inner list class for holding multiple entries for attribute protocol.
 class Protocol_package.Software_list
          Inner list class for holding multiple entries for attribute software.
 
Field Summary
 Protocol_package.Hardware_list hardware_list
          Hardware represents the hardware used.
 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 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
 boolean emptyMAGEobject()
           
 Hardware getFromHardware_list(int position)
          Method to get Hardware from Hardware_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
 java.lang.String getModelClassName()
           
 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 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 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 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 This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

hardware_list

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


software_list

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


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.

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

Parameters:
atts: - the attribute list.
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.

Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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.

Throws:
java.io.IOException

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.

Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()

setHardware_list

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

Parameters:
value - to set

getHardware_list

public Protocol_package.Hardware_list getHardware_list()
Get method for hardware_list

Returns:
value of the attribute

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


setSoftware_list

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

Parameters:
value - to set

getSoftware_list

public Protocol_package.Software_list getSoftware_list()
Get method for software_list

Returns:
value of the attribute

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


setProtocol_list

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

Parameters:
value - to set

getProtocol_list

public Protocol_package.Protocol_list getProtocol_list()
Get method for protocol_list

Returns:
value of the attribute

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