org.biomage.Experiment
Class ExperimentalFactor

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.Experiment.ExperimentalFactor

All Implemented Interfaces:

HasAuditTrail, HasCategory, HasDescriptions, HasFactorValues, HasPropertySets, HasSecurity, java.io.Serializable

public class ExperimentalFactor

extends Identifiable

implements java.io.Serializable, HasFactorValues, HasCategory

ExperimentFactors are the dependent variables of an experiment (e.g. time, glucose concentration, ...).

See Also:

Serialized Form

Nested Class Summary

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

HasFactorValues.FactorValues_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 OntologyEntry	category The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).
protected HasFactorValues.FactorValues_list	factorValues The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ExperimentalFactor()
Default constructor.

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

Method Summary

void	addToFactorValues(FactorValue factorValue) Method to add FactorValue to FactorValues_list
void	addToFactorValues(int position, FactorValue factorValue) Method to add FactorValue at position to FactorValues_list
OntologyEntry	getCategory() Get method for category
HasFactorValues.FactorValues_list	getFactorValues() Get method for factorValues
FactorValue	getFromFactorValues(int position) Method to get FactorValue from FactorValues_list
void	removeElementAtFromFactorValues(int position) Method to remove by position from FactorValues_list
void	removeFromFactorValues(FactorValue factorValue) Method to remove first FactorValue from FactorValues_list
void	setCategory(OntologyEntry category) Set method for category
void	setFactorValues(HasFactorValues.FactorValues_list factorValues) Set method for factorValues
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

category

protected OntologyEntry category

The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).

factorValues

protected HasFactorValues.FactorValues_list factorValues

The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.

Constructor Detail

ExperimentalFactor

public ExperimentalFactor()

Default constructor.

ExperimentalFactor

public ExperimentalFactor(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

setCategory

public void setCategory(OntologyEntry category)

Set method for category

Specified by:

setCategory in interface HasCategory

getCategory

public OntologyEntry getCategory()

Get method for category

Specified by:

getCategory in interface HasCategory

Returns:

value of the attribute

setFactorValues

public void setFactorValues(HasFactorValues.FactorValues_list factorValues)

Set method for factorValues

Specified by:

setFactorValues in interface HasFactorValues

getFactorValues

public HasFactorValues.FactorValues_list getFactorValues()

Get method for factorValues

Specified by:

getFactorValues in interface HasFactorValues

Returns:

value of the attribute

addToFactorValues

public void addToFactorValues(FactorValue factorValue)

Method to add FactorValue to FactorValues_list

Specified by:

addToFactorValues in interface HasFactorValues

addToFactorValues

public void addToFactorValues(int position,
                              FactorValue factorValue)

Method to add FactorValue at position to FactorValues_list

Specified by:

addToFactorValues in interface HasFactorValues

getFromFactorValues

public FactorValue getFromFactorValues(int position)

Method to get FactorValue from FactorValues_list

Specified by:

getFromFactorValues in interface HasFactorValues

removeElementAtFromFactorValues

public void removeElementAtFromFactorValues(int position)

Method to remove by position from FactorValues_list

Specified by:

removeElementAtFromFactorValues in interface HasFactorValues

removeFromFactorValues

public void removeFromFactorValues(FactorValue factorValue)

Method to remove first FactorValue from FactorValues_list

Specified by:

removeFromFactorValues in interface HasFactorValues