org.biomage.Experiment
Class ExperimentalFactor

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.ExperimentalFactor
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAnnotations, HasAuditTrail, HasCategory, HasDescriptions, HasFactorValues, HasPropertySets, HasSecurity

public class ExperimentalFactor
extends Identifiable
implements java.io.Serializable, HasFactorValues, HasCategory, HasAnnotations

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

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFactorValues
HasFactorValues.FactorValues_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAnnotations
HasAnnotations.Annotations_list
 
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  java.util.List annotations
          Allows describing additional information such as concentration of Tamoxafin with a CASRegistry #.
protected  OntologyEntry category
          The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).
protected  java.util.List factorValues
          The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
ExperimentalFactor()
          Default constructor.
ExperimentalFactor(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToAnnotations(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Annotations_list
 void addToAnnotations(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Annotations_list
 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
 boolean emptyMAGEobject()
           
 HasAnnotations.Annotations_list getAnnotations()
          Get method for annotations
 OntologyEntry getCategory()
          Get method for category
 HasFactorValues.FactorValues_list getFactorValues()
          Get method for factorValues
 OntologyEntry getFromAnnotations(int position)
          Method to get OntologyEntry from Annotations_list
 FactorValue getFromFactorValues(int position)
          Method to get FactorValue from FactorValues_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromAnnotations(int position)
          Method to remove by position from Annotations_list
 void removeElementAtFromFactorValues(int position)
          Method to remove by position from FactorValues_list
 void removeFromAnnotations(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Annotations_list
 void removeFromFactorValues(FactorValue factorValue)
          Method to remove first FactorValue from FactorValues_list
 void setAnnotations(HasAnnotations.Annotations_list annotations)
          Set method for annotations
 void setAttributes(org.xml.sax.Attributes atts)
           
 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, 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

category

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


factorValues

protected java.util.List factorValues
The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.


annotations

protected java.util.List annotations
Allows describing additional information such as concentration of Tamoxafin with a CASRegistry #.

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

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

setCategory

public void setCategory(OntologyEntry category)
Set method for category

Specified by:
setCategory in interface HasCategory
Parameters:
value - to set

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
Parameters:
value - to set

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

setAnnotations

public void setAnnotations(HasAnnotations.Annotations_list annotations)
Set method for annotations

Specified by:
setAnnotations in interface HasAnnotations
Parameters:
value - to set

getAnnotations

public HasAnnotations.Annotations_list getAnnotations()
Get method for annotations

Specified by:
getAnnotations in interface HasAnnotations
Returns:
value of the attribute

addToAnnotations

public void addToAnnotations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Annotations_list

Specified by:
addToAnnotations in interface HasAnnotations

addToAnnotations

public void addToAnnotations(int position,
                             OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Annotations_list

Specified by:
addToAnnotations in interface HasAnnotations

getFromAnnotations

public OntologyEntry getFromAnnotations(int position)
Method to get OntologyEntry from Annotations_list

Specified by:
getFromAnnotations in interface HasAnnotations

removeElementAtFromAnnotations

public void removeElementAtFromAnnotations(int position)
Method to remove by position from Annotations_list

Specified by:
removeElementAtFromAnnotations in interface HasAnnotations

removeFromAnnotations

public void removeFromAnnotations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Annotations_list

Specified by:
removeFromAnnotations in interface HasAnnotations