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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:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasCategory, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasFactorValues, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

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public class ExperimentalFactor

extends org.biomage.Common.Identifiable

implements java.io.Serializable, org.biomage.Interface.HasFactorValues, org.biomage.Interface.HasCategory

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

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Nested Class Summary

 

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

org.biomage.Interface.HasFactorValues.FactorValues_list

 

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

 

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

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
org.biomage.Description.OntologyEntry	getCategory()           Get method for category
org.biomage.Interface.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(org.biomage.Description.OntologyEntry category)           Set method for category
void	setFactorValues(org.biomage.Interface.HasFactorValues.FactorValues_list factorValues)           Set method for factorValues
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

factorValues

private org.biomage.Interface.HasFactorValues.FactorValues_list factorValues

The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.

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category

private org.biomage.Description.OntologyEntry category

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

Constructor Detail

ExperimentalFactor

public ExperimentalFactor()

Default constructor.

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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.

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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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setFactorValues

public void setFactorValues(org.biomage.Interface.HasFactorValues.FactorValues_list factorValues)

Set method for factorValues

Specified by:

setFactorValues in interface org.biomage.Interface.HasFactorValues

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getFactorValues

public org.biomage.Interface.HasFactorValues.FactorValues_list getFactorValues()

Get method for factorValues

Specified by:

getFactorValues in interface org.biomage.Interface.HasFactorValues

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addToFactorValues

public void addToFactorValues(FactorValue factorValue)

Method to add FactorValue to FactorValues_list

Specified by:

addToFactorValues in interface org.biomage.Interface.HasFactorValues

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addToFactorValues

public void addToFactorValues(int position,
                              FactorValue factorValue)

Method to add FactorValue at position to FactorValues_list

Specified by:

addToFactorValues in interface org.biomage.Interface.HasFactorValues

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getFromFactorValues

public FactorValue getFromFactorValues(int position)

Method to get FactorValue from FactorValues_list

Specified by:

getFromFactorValues in interface org.biomage.Interface.HasFactorValues

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removeElementAtFromFactorValues

public void removeElementAtFromFactorValues(int position)

Method to remove by position from FactorValues_list

Specified by:

removeElementAtFromFactorValues in interface org.biomage.Interface.HasFactorValues

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removeFromFactorValues

public void removeFromFactorValues(FactorValue factorValue)

Method to remove first FactorValue from FactorValues_list

Specified by:

removeFromFactorValues in interface org.biomage.Interface.HasFactorValues

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setCategory

public void setCategory(org.biomage.Description.OntologyEntry category)

Set method for category

Specified by:

setCategory in interface org.biomage.Interface.HasCategory

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getCategory

public org.biomage.Description.OntologyEntry getCategory()

Get method for category

Specified by:

getCategory in interface org.biomage.Interface.HasCategory

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ Experiment overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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