org.biomage.Experiment
Class ExperimentDesign

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Experiment.ExperimentDesign
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasExperimentalFactors, HasNormalizationDescription, HasPropertySets, HasQualityControlDescription, HasReplicateDescription, HasSecurity, HasTopLevelBioAssays, HasTypes

public class ExperimentDesign
extends Describable
implements java.io.Serializable, HasTopLevelBioAssays, HasExperimentalFactors, HasReplicateDescription, HasQualityControlDescription, HasNormalizationDescription, HasTypes

The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTopLevelBioAssays
HasTopLevelBioAssays.TopLevelBioAssays_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasExperimentalFactors
HasExperimentalFactors.ExperimentalFactors_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTypes
HasTypes.Types_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 experimentalFactors
          The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays.
protected  Description normalizationDescription
          Description of the normalization strategy of the Experiment.
protected  Description qualityControlDescription
          Description of the quality control aspects of the Experiment.
protected  Description replicateDescription
          Description of the replicate strategy of the Experiment.
protected  java.util.List topLevelBioAssays
          The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)
protected  java.util.List types
          Classification of an experiment.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
ExperimentDesign()
          Default constructor.
ExperimentDesign(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToExperimentalFactors(ExperimentalFactor experimentalFactor)
          Method to add ExperimentalFactor to ExperimentalFactors_list
 void addToExperimentalFactors(int position, ExperimentalFactor experimentalFactor)
          Method to add ExperimentalFactor at position to ExperimentalFactors_list
 void addToTopLevelBioAssays(BioAssay bioAssay)
          Method to add BioAssay to TopLevelBioAssays_list
 void addToTopLevelBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to TopLevelBioAssays_list
 void addToTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Types_list
 void addToTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Types_list
 boolean emptyMAGEobject()
           
 HasExperimentalFactors.ExperimentalFactors_list getExperimentalFactors()
          Get method for experimentalFactors
 ExperimentalFactor getFromExperimentalFactors(int position)
          Method to get ExperimentalFactor from ExperimentalFactors_list
 BioAssay getFromTopLevelBioAssays(int position)
          Method to get BioAssay from TopLevelBioAssays_list
 OntologyEntry getFromTypes(int position)
          Method to get OntologyEntry from Types_list
 java.lang.String getModelClassName()
           
 Description getNormalizationDescription()
          Get method for normalizationDescription
 Description getQualityControlDescription()
          Get method for qualityControlDescription
 Description getReplicateDescription()
          Get method for replicateDescription
 HasTopLevelBioAssays.TopLevelBioAssays_list getTopLevelBioAssays()
          Get method for topLevelBioAssays
 HasTypes.Types_list getTypes()
          Get method for types
 void removeElementAtFromExperimentalFactors(int position)
          Method to remove by position from ExperimentalFactors_list
 void removeElementAtFromTopLevelBioAssays(int position)
          Method to remove by position from TopLevelBioAssays_list
 void removeElementAtFromTypes(int position)
          Method to remove by position from Types_list
 void removeFromExperimentalFactors(ExperimentalFactor experimentalFactor)
          Method to remove first ExperimentalFactor from ExperimentalFactors_list
 void removeFromTopLevelBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from TopLevelBioAssays_list
 void removeFromTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Types_list
 void setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list experimentalFactors)
          Set method for experimentalFactors
 void setNormalizationDescription(Description normalizationDescription)
          Set method for normalizationDescription
 void setQualityControlDescription(Description qualityControlDescription)
          Set method for qualityControlDescription
 void setReplicateDescription(Description replicateDescription)
          Set method for replicateDescription
 void setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays)
          Set method for topLevelBioAssays
 void setTypes(HasTypes.Types_list types)
          Set method for types
 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.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAttributes, 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, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

types

protected java.util.List types
Classification of an experiment. For example 'normal vs. diseased', 'treated vs. untreated', 'time course', 'tiling', etc.


topLevelBioAssays

protected java.util.List topLevelBioAssays
The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)


experimentalFactors

protected java.util.List experimentalFactors
The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays.


qualityControlDescription

protected Description qualityControlDescription
Description of the quality control aspects of the Experiment.


normalizationDescription

protected Description normalizationDescription
Description of the normalization strategy of the Experiment.


replicateDescription

protected Description replicateDescription
Description of the replicate strategy of the Experiment.

Constructor Detail

ExperimentDesign

public ExperimentDesign()
Default constructor.


ExperimentDesign

public ExperimentDesign(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

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 Describable
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 Describable
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 Describable
Throws:
java.io.IOException

getModelClassName

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

setTypes

public void setTypes(HasTypes.Types_list types)
Set method for types

Specified by:
setTypes in interface HasTypes
Parameters:
value - to set

getTypes

public HasTypes.Types_list getTypes()
Get method for types

Specified by:
getTypes in interface HasTypes
Returns:
value of the attribute

addToTypes

public void addToTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list

Specified by:
addToTypes in interface HasTypes

addToTypes

public void addToTypes(int position,
                       OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list

Specified by:
addToTypes in interface HasTypes

getFromTypes

public OntologyEntry getFromTypes(int position)
Method to get OntologyEntry from Types_list

Specified by:
getFromTypes in interface HasTypes

removeElementAtFromTypes

public void removeElementAtFromTypes(int position)
Method to remove by position from Types_list

Specified by:
removeElementAtFromTypes in interface HasTypes

removeFromTypes

public void removeFromTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list

Specified by:
removeFromTypes in interface HasTypes

setTopLevelBioAssays

public void setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays)
Set method for topLevelBioAssays

Specified by:
setTopLevelBioAssays in interface HasTopLevelBioAssays
Parameters:
value - to set

getTopLevelBioAssays

public HasTopLevelBioAssays.TopLevelBioAssays_list getTopLevelBioAssays()
Get method for topLevelBioAssays

Specified by:
getTopLevelBioAssays in interface HasTopLevelBioAssays
Returns:
value of the attribute

addToTopLevelBioAssays

public void addToTopLevelBioAssays(BioAssay bioAssay)
Method to add BioAssay to TopLevelBioAssays_list

Specified by:
addToTopLevelBioAssays in interface HasTopLevelBioAssays

addToTopLevelBioAssays

public void addToTopLevelBioAssays(int position,
                                   BioAssay bioAssay)
Method to add BioAssay at position to TopLevelBioAssays_list

Specified by:
addToTopLevelBioAssays in interface HasTopLevelBioAssays

getFromTopLevelBioAssays

public BioAssay getFromTopLevelBioAssays(int position)
Method to get BioAssay from TopLevelBioAssays_list

Specified by:
getFromTopLevelBioAssays in interface HasTopLevelBioAssays

removeElementAtFromTopLevelBioAssays

public void removeElementAtFromTopLevelBioAssays(int position)
Method to remove by position from TopLevelBioAssays_list

Specified by:
removeElementAtFromTopLevelBioAssays in interface HasTopLevelBioAssays

removeFromTopLevelBioAssays

public void removeFromTopLevelBioAssays(BioAssay bioAssay)
Method to remove first BioAssay from TopLevelBioAssays_list

Specified by:
removeFromTopLevelBioAssays in interface HasTopLevelBioAssays

setExperimentalFactors

public void setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list experimentalFactors)
Set method for experimentalFactors

Specified by:
setExperimentalFactors in interface HasExperimentalFactors
Parameters:
value - to set

getExperimentalFactors

public HasExperimentalFactors.ExperimentalFactors_list getExperimentalFactors()
Get method for experimentalFactors

Specified by:
getExperimentalFactors in interface HasExperimentalFactors
Returns:
value of the attribute

addToExperimentalFactors

public void addToExperimentalFactors(ExperimentalFactor experimentalFactor)
Method to add ExperimentalFactor to ExperimentalFactors_list

Specified by:
addToExperimentalFactors in interface HasExperimentalFactors

addToExperimentalFactors

public void addToExperimentalFactors(int position,
                                     ExperimentalFactor experimentalFactor)
Method to add ExperimentalFactor at position to ExperimentalFactors_list

Specified by:
addToExperimentalFactors in interface HasExperimentalFactors

getFromExperimentalFactors

public ExperimentalFactor getFromExperimentalFactors(int position)
Method to get ExperimentalFactor from ExperimentalFactors_list

Specified by:
getFromExperimentalFactors in interface HasExperimentalFactors

removeElementAtFromExperimentalFactors

public void removeElementAtFromExperimentalFactors(int position)
Method to remove by position from ExperimentalFactors_list

Specified by:
removeElementAtFromExperimentalFactors in interface HasExperimentalFactors

removeFromExperimentalFactors

public void removeFromExperimentalFactors(ExperimentalFactor experimentalFactor)
Method to remove first ExperimentalFactor from ExperimentalFactors_list

Specified by:
removeFromExperimentalFactors in interface HasExperimentalFactors

setQualityControlDescription

public void setQualityControlDescription(Description qualityControlDescription)
Set method for qualityControlDescription

Specified by:
setQualityControlDescription in interface HasQualityControlDescription
Parameters:
value - to set

getQualityControlDescription

public Description getQualityControlDescription()
Get method for qualityControlDescription

Specified by:
getQualityControlDescription in interface HasQualityControlDescription
Returns:
value of the attribute

setNormalizationDescription

public void setNormalizationDescription(Description normalizationDescription)
Set method for normalizationDescription

Specified by:
setNormalizationDescription in interface HasNormalizationDescription
Parameters:
value - to set

getNormalizationDescription

public Description getNormalizationDescription()
Get method for normalizationDescription

Specified by:
getNormalizationDescription in interface HasNormalizationDescription
Returns:
value of the attribute

setReplicateDescription

public void setReplicateDescription(Description replicateDescription)
Set method for replicateDescription

Specified by:
setReplicateDescription in interface HasReplicateDescription
Parameters:
value - to set

getReplicateDescription

public Description getReplicateDescription()
Get method for replicateDescription

Specified by:
getReplicateDescription in interface HasReplicateDescription
Returns:
value of the attribute