org.biomage.Experiment
Class FactorValue

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.Experiment.FactorValue
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasExperimentalFactor, HasMeasurement, HasPropertySets, HasSecurity, HasValue

public class FactorValue
extends Identifiable
implements java.io.Serializable, HasExperimentalFactor, HasMeasurement, HasValue

The value for a ExperimentalFactor

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  ExperimentalFactor experimentalFactor
          The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.
protected  Measurement measurement
          The measured value for this factor.
protected  OntologyEntry value
          Allows a more complex value to be specified for a FactorValue than a simple Measurement.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
FactorValue()
          Default constructor.
FactorValue(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 ExperimentalFactor getExperimentalFactor()
          Get method for experimentalFactor
 Measurement getMeasurement()
          Get method for measurement
 java.lang.String getModelClassName()
           
 OntologyEntry getValue()
          Get method for value
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setExperimentalFactor(ExperimentalFactor experimentalFactor)
          Set method for experimentalFactor
 void setMeasurement(Measurement measurement)
          Set method for measurement
 void setValue(OntologyEntry value)
          Set method for value
 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, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

experimentalFactor

protected ExperimentalFactor experimentalFactor
The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.


measurement

protected Measurement measurement
The measured value for this factor.


value

protected OntologyEntry value
Allows a more complex value to be specified for a FactorValue than a simple Measurement.

Constructor Detail

FactorValue

public FactorValue()
Default constructor.


FactorValue

public FactorValue(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

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

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
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.

Overrides:
writeAttributes in class Identifiable
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.

Overrides:
writeAssociations in class Identifiable
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Identifiable

setExperimentalFactor

public void setExperimentalFactor(ExperimentalFactor experimentalFactor)
Set method for experimentalFactor

Specified by:
setExperimentalFactor in interface HasExperimentalFactor
Parameters:
value - to set

getExperimentalFactor

public ExperimentalFactor getExperimentalFactor()
Get method for experimentalFactor

Specified by:
getExperimentalFactor in interface HasExperimentalFactor
Returns:
value of the attribute

setMeasurement

public void setMeasurement(Measurement measurement)
Set method for measurement

Specified by:
setMeasurement in interface HasMeasurement
Parameters:
value - to set

getMeasurement

public Measurement getMeasurement()
Get method for measurement

Specified by:
getMeasurement in interface HasMeasurement
Returns:
value of the attribute

setValue

public void setValue(OntologyEntry value)
Set method for value

Specified by:
setValue in interface HasValue
Parameters:
value - to set

getValue

public OntologyEntry getValue()
Get method for value

Specified by:
getValue in interface HasValue
Returns:
value of the attribute