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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:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDataType, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasUnit, java.io.Serializable

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public class Parameter

extends org.biomage.Common.Identifiable

implements java.io.Serializable, org.biomage.Interface.HasDataType, org.biomage.Interface.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.

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Nested Class Summary

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Description.OntologyEntry	dataType           The type of data generated by the parameter i.e.
private  org.biomage.Measurement.Unit	unit           Unit the value is associated with

 

Fields inherited from class org.biomage.Common.Identifiable

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

Parameter()           Default constructor.

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

 

Method Summary
org.biomage.Description.OntologyEntry	getDataType()           Get method for dataType
org.biomage.Measurement.Unit	getUnit()           Get method for unit
void	setDataType(org.biomage.Description.OntologyEntry dataType)           Set method for dataType
void	setUnit(org.biomage.Measurement.Unit unit)           Set method for unit
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 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

dataType

private org.biomage.Description.OntologyEntry dataType

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

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unit

private org.biomage.Measurement.Unit unit

Unit the value is associated with

Constructor Detail

Parameter

public Parameter()

Default constructor.

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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.

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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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setDataType

public void setDataType(org.biomage.Description.OntologyEntry dataType)

Set method for dataType

Specified by:

setDataType in interface org.biomage.Interface.HasDataType

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getDataType

public org.biomage.Description.OntologyEntry getDataType()

Get method for dataType

Specified by:

getDataType in interface org.biomage.Interface.HasDataType

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setUnit

public void setUnit(org.biomage.Measurement.Unit unit)

Set method for unit

Specified by:

setUnit in interface org.biomage.Interface.HasUnit

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getUnit

public org.biomage.Measurement.Unit getUnit()

Get method for unit

Specified by:

getUnit in interface org.biomage.Interface.HasUnit

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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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