org.biomage.Protocol
Class ParameterizableApplication

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Protocol.ParameterizableApplication

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasParameterValues, HasPropertySets, HasSecurity, java.io.Serializable

Direct Known Subclasses:

HardwareApplication, ProtocolApplication, SoftwareApplication

public abstract class ParameterizableApplication

extends Describable

implements java.io.Serializable, HasParameterValues

The interface that is the use of a Parameterizable class.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasParameterValues

HasParameterValues.ParameterValues_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasParameterValues.ParameterValues_list

parameterValues The parameter values for this Parameterizable Application.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ParameterizableApplication()
Default constructor.

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

Method Summary

void	addToParameterValues(int position, ParameterValue parameterValue) Method to add ParameterValue at position to ParameterValues_list
void	addToParameterValues(ParameterValue parameterValue) Method to add ParameterValue to ParameterValues_list
ParameterValue	getFromParameterValues(int position) Method to get ParameterValue from ParameterValues_list
HasParameterValues.ParameterValues_list	getParameterValues() Get method for parameterValues
void	removeElementAtFromParameterValues(int position) Method to remove by position from ParameterValues_list
void	removeFromParameterValues(ParameterValue parameterValue) Method to remove first ParameterValue from ParameterValues_list
void	setParameterValues(HasParameterValues.ParameterValues_list parameterValues) Set method for parameterValues
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 org.biomage.Common.Describable

addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity

Methods inherited from class org.biomage.Common.Extendable

addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

parameterValues

protected HasParameterValues.ParameterValues_list parameterValues

The parameter values for this Parameterizable Application.

Constructor Detail

ParameterizableApplication

public ParameterizableApplication()

Default constructor.

ParameterizableApplication

public ParameterizableApplication(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.

Overrides:

writeMAGEML in class Describable

java.io.IOException

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.

Overrides:

writeAttributes in class Describable

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.

Overrides:

writeAssociations in class Describable

java.io.IOException

setParameterValues

public void setParameterValues(HasParameterValues.ParameterValues_list parameterValues)

Set method for parameterValues

Specified by:

setParameterValues in interface HasParameterValues

getParameterValues

public HasParameterValues.ParameterValues_list getParameterValues()

Get method for parameterValues

Specified by:

getParameterValues in interface HasParameterValues

Returns:

value of the attribute

addToParameterValues

public void addToParameterValues(ParameterValue parameterValue)

Method to add ParameterValue to ParameterValues_list

Specified by:

addToParameterValues in interface HasParameterValues

addToParameterValues

public void addToParameterValues(int position,
                                 ParameterValue parameterValue)

Method to add ParameterValue at position to ParameterValues_list

Specified by:

addToParameterValues in interface HasParameterValues

getFromParameterValues

public ParameterValue getFromParameterValues(int position)

Method to get ParameterValue from ParameterValues_list

Specified by:

getFromParameterValues in interface HasParameterValues

removeElementAtFromParameterValues

public void removeElementAtFromParameterValues(int position)

Method to remove by position from ParameterValues_list

Specified by:

removeElementAtFromParameterValues in interface HasParameterValues

removeFromParameterValues

public void removeFromParameterValues(ParameterValue parameterValue)

Method to remove first ParameterValue from ParameterValues_list

Specified by:

removeFromParameterValues in interface HasParameterValues