org.biomage.Protocol
Class Parameter

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

All Implemented Interfaces:

HasAuditTrail, HasDataType, HasDescriptions, HasPropertySets, HasSecurity, HasUnit, java.io.Serializable

public class Parameter

extends Identifiable

implements java.io.Serializable, HasDataType, HasUnit

A Parameter is a replaceable value in a Parameterizable class. Examples of Parameters include: scanning wavelength, laser power, centrifuge speed, multiplicative errors, the number of input nodes to a SOM, and PCR temperatures.

See Also:

Serialized Form

Nested Class Summary

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 OntologyEntry	dataType The type of data generated by the parameter i.e.
protected Unit	unit Unit the value is associated with

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Parameter()
Default constructor.

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

Method Summary

OntologyEntry	getDataType() Get method for dataType
Unit	getUnit() Get method for unit
void	setDataType(OntologyEntry dataType) Set method for dataType
void	setUnit(Unit unit) Set method for unit
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.Identifiable

getIdentifier, getName, setIdentifier, setName

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

unit

protected Unit unit

Unit the value is associated with

dataType

protected OntologyEntry dataType

The type of data generated by the parameter i.e. Boolean, float, etc...

Constructor Detail

Parameter

public Parameter()

Default constructor.

Parameter

public Parameter(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 Identifiable

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 Identifiable

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 Identifiable

java.io.IOException

setUnit

public void setUnit(Unit unit)

Set method for unit

Specified by:

setUnit in interface HasUnit

getUnit

public Unit getUnit()

Get method for unit

Specified by:

getUnit in interface HasUnit

Returns:

value of the attribute

setDataType

public void setDataType(OntologyEntry dataType)

Set method for dataType

Specified by:

setDataType in interface HasDataType

getDataType

public OntologyEntry getDataType()

Get method for dataType

Specified by:

getDataType in interface HasDataType

Returns:

value of the attribute