org.biomage.Experiment
Class Experiment

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.Experiment
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAnalysisResults, HasAuditTrail, HasBioAssayData, HasBioAssays, HasDescriptions, HasExperimentDesigns, HasPropertySets, HasProviders, HasSecurity

public class Experiment
extends Identifiable
implements java.io.Serializable, HasAnalysisResults, HasBioAssays, HasProviders, HasBioAssayData, HasExperimentDesigns

The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAnalysisResults
HasAnalysisResults.AnalysisResults_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssays
HasBioAssays.BioAssays_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProviders
HasProviders.Providers_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayData
HasBioAssayData.BioAssayData_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasExperimentDesigns
HasExperimentDesigns.ExperimentDesigns_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 analysisResults
          The results of analyzing the data, typically with a clustering algorithm.
protected  java.util.List bioAssayData
          The collection of BioAssayDatas for this Experiment.
protected  java.util.List bioAssays
          The collection of BioAssays for this Experiment.
protected  boolean deleted
          caARRAY-specific marker if this Experiment is deleted.
protected  java.util.List experimentDesigns
          The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.
protected  java.util.List providerRoles
          The providers of the Experiment that have a role which describes how he/she contributes the experiment, e.g.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Experiment()
          Default constructor.
Experiment(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToAnalysisResults(BioAssayDataCluster bioAssayDataCluster)
          Method to add BioAssayDataCluster to AnalysisResults_list
 void addToAnalysisResults(int position, BioAssayDataCluster bioAssayDataCluster)
          Method to add BioAssayDataCluster at position to AnalysisResults_list
 void addToBioAssayData(BioAssayData bioAssayData)
          Method to add BioAssayData to BioAssayData_list
 void addToBioAssayData(int position, BioAssayData bioAssayData)
          Method to add BioAssayData at position to BioAssayData_list
 void addToBioAssays(BioAssay bioAssay)
          Method to add BioAssay to BioAssays_list
 void addToBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to BioAssays_list
 void addToExperimentDesigns(ExperimentDesign experimentDesign)
          Method to add ExperimentDesign to ExperimentDesigns_list
 void addToExperimentDesigns(int position, ExperimentDesign experimentDesign)
          Method to add ExperimentDesign at position to ExperimentDesigns_list
 void addToProviderRoles(ExperimentProviderRole providerRole)
          Adds a provider of this experiment that has a role
 void addToProviderRoles(int position, ExperimentProviderRole providerRole)
          Adds a provider of this experiment that has a role
 void addToProviders(Contact contact)
          Method to add Contact to Providers_list
 void addToProviders(int position, Contact contact)
          Method to add Contact at position to Providers_list
 boolean emptyMAGEobject()
           
 HasAnalysisResults.AnalysisResults_list getAnalysisResults()
          Get method for analysisResults
 HasBioAssayData.BioAssayData_list getBioAssayData()
          Get method for bioAssayData
 HasBioAssays.BioAssays_list getBioAssays()
          Get method for bioAssays
 HasExperimentDesigns.ExperimentDesigns_list getExperimentDesigns()
          Get method for experimentDesigns
 BioAssayDataCluster getFromAnalysisResults(int position)
          Method to get BioAssayDataCluster from AnalysisResults_list
 BioAssayData getFromBioAssayData(int position)
          Method to get BioAssayData from BioAssayData_list
 BioAssay getFromBioAssays(int position)
          Method to get BioAssay from BioAssays_list
 ExperimentDesign getFromExperimentDesigns(int position)
          Method to get ExperimentDesign from ExperimentDesigns_list
 ExperimentProviderRole getFromProviderRoles(int position)
           
 Contact getFromProviders(int position)
          Method to get Contact from Providers_list
 java.lang.String getModelClassName()
           
 java.util.ArrayList getProviderRoles()
           
 HasProviders.Providers_list getProviders()
          Get method for providers
 boolean isDeleted()
           
 void removeElementAtFromAnalysisResults(int position)
          Method to remove by position from AnalysisResults_list
 void removeElementAtFromBioAssayData(int position)
          Method to remove by position from BioAssayData_list
 void removeElementAtFromBioAssays(int position)
          Method to remove by position from BioAssays_list
 void removeElementAtFromExperimentDesigns(int position)
          Method to remove by position from ExperimentDesigns_list
 void removeElementAtFromProviders(int position)
          Method to remove by position from Providers_list
 void removeFromAnalysisResults(BioAssayDataCluster bioAssayDataCluster)
          Method to remove first BioAssayDataCluster from AnalysisResults_list
 void removeFromBioAssayData(BioAssayData bioAssayData)
          Method to remove first BioAssayData from BioAssayData_list
 void removeFromBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from BioAssays_list
 void removeFromExperimentDesigns(ExperimentDesign experimentDesign)
          Method to remove first ExperimentDesign from ExperimentDesigns_list
 void removeFromProviderRoles(ExperimentProviderRole providerRole)
           
 void removeFromProviders(Contact contact)
          Method to remove first Contact from Providers_list
 void setAnalysisResults(HasAnalysisResults.AnalysisResults_list analysisResults)
          Set method for analysisResults
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setBioAssayData(HasBioAssayData.BioAssayData_list bioAssayData)
          Set method for bioAssayData
 void setBioAssays(HasBioAssays.BioAssays_list bioAssays)
          Set method for bioAssays
 void setDeleted(boolean deleted)
          Sets if this Experiment is deleted.
 void setExperimentDesigns(HasExperimentDesigns.ExperimentDesigns_list experimentDesigns)
          Set method for experimentDesigns
 void setProviderRoles(java.util.ArrayList providerRoles)
          The specified providerRoles must be instantiable List subclass for creation by reflection to work.
 void setProviders(HasProviders.Providers_list providers)
          Set method for providers
 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

providerRoles

protected java.util.List providerRoles
The providers of the Experiment that have a role which describes how he/she contributes the experiment, e.g. investigator, primary contact, etc.


analysisResults

protected java.util.List analysisResults
The results of analyzing the data, typically with a clustering algorithm.


bioAssayData

protected java.util.List bioAssayData
The collection of BioAssayDatas for this Experiment.


bioAssays

protected java.util.List bioAssays
The collection of BioAssays for this Experiment.


experimentDesigns

protected java.util.List experimentDesigns
The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.


deleted

protected boolean deleted
caARRAY-specific marker if this Experiment is deleted.

Constructor Detail

Experiment

public Experiment()
Default constructor.


Experiment

public Experiment(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

setProviders

public void setProviders(HasProviders.Providers_list providers)
Set method for providers

Specified by:
setProviders in interface HasProviders
Parameters:
value - to set

setProviderRoles

public void setProviderRoles(java.util.ArrayList providerRoles)
The specified providerRoles must be instantiable List subclass for creation by reflection to work. tranp (caARRAY) 8/4/04

Parameters:
providerRoles -

getProviders

public HasProviders.Providers_list getProviders()
Get method for providers

Specified by:
getProviders in interface HasProviders
Returns:
value of the attribute

getProviderRoles

public java.util.ArrayList getProviderRoles()

addToProviders

public void addToProviders(Contact contact)
Method to add Contact to Providers_list

Specified by:
addToProviders in interface HasProviders

addToProviderRoles

public void addToProviderRoles(ExperimentProviderRole providerRole)
Adds a provider of this experiment that has a role

Parameters:
providerRole - - A provider who has a role such as investigator, primary contact, etc.

addToProviders

public void addToProviders(int position,
                           Contact contact)
Method to add Contact at position to Providers_list

Specified by:
addToProviders in interface HasProviders

addToProviderRoles

public void addToProviderRoles(int position,
                               ExperimentProviderRole providerRole)
Adds a provider of this experiment that has a role


getFromProviders

public Contact getFromProviders(int position)
Method to get Contact from Providers_list

Specified by:
getFromProviders in interface HasProviders

getFromProviderRoles

public ExperimentProviderRole getFromProviderRoles(int position)

removeElementAtFromProviders

public void removeElementAtFromProviders(int position)
Method to remove by position from Providers_list

Specified by:
removeElementAtFromProviders in interface HasProviders

removeFromProviders

public void removeFromProviders(Contact contact)
Method to remove first Contact from Providers_list

Specified by:
removeFromProviders in interface HasProviders

removeFromProviderRoles

public void removeFromProviderRoles(ExperimentProviderRole providerRole)

setAnalysisResults

public void setAnalysisResults(HasAnalysisResults.AnalysisResults_list analysisResults)
Set method for analysisResults

Specified by:
setAnalysisResults in interface HasAnalysisResults
Parameters:
value - to set

getAnalysisResults

public HasAnalysisResults.AnalysisResults_list getAnalysisResults()
Get method for analysisResults

Specified by:
getAnalysisResults in interface HasAnalysisResults
Returns:
value of the attribute

addToAnalysisResults

public void addToAnalysisResults(BioAssayDataCluster bioAssayDataCluster)
Method to add BioAssayDataCluster to AnalysisResults_list

Specified by:
addToAnalysisResults in interface HasAnalysisResults

addToAnalysisResults

public void addToAnalysisResults(int position,
                                 BioAssayDataCluster bioAssayDataCluster)
Method to add BioAssayDataCluster at position to AnalysisResults_list

Specified by:
addToAnalysisResults in interface HasAnalysisResults

getFromAnalysisResults

public BioAssayDataCluster getFromAnalysisResults(int position)
Method to get BioAssayDataCluster from AnalysisResults_list

Specified by:
getFromAnalysisResults in interface HasAnalysisResults

removeElementAtFromAnalysisResults

public void removeElementAtFromAnalysisResults(int position)
Method to remove by position from AnalysisResults_list

Specified by:
removeElementAtFromAnalysisResults in interface HasAnalysisResults

removeFromAnalysisResults

public void removeFromAnalysisResults(BioAssayDataCluster bioAssayDataCluster)
Method to remove first BioAssayDataCluster from AnalysisResults_list

Specified by:
removeFromAnalysisResults in interface HasAnalysisResults

setBioAssayData

public void setBioAssayData(HasBioAssayData.BioAssayData_list bioAssayData)
Set method for bioAssayData

Specified by:
setBioAssayData in interface HasBioAssayData
Parameters:
value - to set

getBioAssayData

public HasBioAssayData.BioAssayData_list getBioAssayData()
Get method for bioAssayData

Specified by:
getBioAssayData in interface HasBioAssayData
Returns:
value of the attribute

addToBioAssayData

public void addToBioAssayData(BioAssayData bioAssayData)
Method to add BioAssayData to BioAssayData_list

Specified by:
addToBioAssayData in interface HasBioAssayData

addToBioAssayData

public void addToBioAssayData(int position,
                              BioAssayData bioAssayData)
Method to add BioAssayData at position to BioAssayData_list

Specified by:
addToBioAssayData in interface HasBioAssayData

getFromBioAssayData

public BioAssayData getFromBioAssayData(int position)
Method to get BioAssayData from BioAssayData_list

Specified by:
getFromBioAssayData in interface HasBioAssayData

removeElementAtFromBioAssayData

public void removeElementAtFromBioAssayData(int position)
Method to remove by position from BioAssayData_list

Specified by:
removeElementAtFromBioAssayData in interface HasBioAssayData

removeFromBioAssayData

public void removeFromBioAssayData(BioAssayData bioAssayData)
Method to remove first BioAssayData from BioAssayData_list

Specified by:
removeFromBioAssayData in interface HasBioAssayData

setBioAssays

public void setBioAssays(HasBioAssays.BioAssays_list bioAssays)
Set method for bioAssays

Specified by:
setBioAssays in interface HasBioAssays
Parameters:
value - to set

getBioAssays

public HasBioAssays.BioAssays_list getBioAssays()
Get method for bioAssays

Specified by:
getBioAssays in interface HasBioAssays
Returns:
value of the attribute

addToBioAssays

public void addToBioAssays(BioAssay bioAssay)
Method to add BioAssay to BioAssays_list

Specified by:
addToBioAssays in interface HasBioAssays

addToBioAssays

public void addToBioAssays(int position,
                           BioAssay bioAssay)
Method to add BioAssay at position to BioAssays_list

Specified by:
addToBioAssays in interface HasBioAssays

getFromBioAssays

public BioAssay getFromBioAssays(int position)
Method to get BioAssay from BioAssays_list

Specified by:
getFromBioAssays in interface HasBioAssays

removeElementAtFromBioAssays

public void removeElementAtFromBioAssays(int position)
Method to remove by position from BioAssays_list

Specified by:
removeElementAtFromBioAssays in interface HasBioAssays

removeFromBioAssays

public void removeFromBioAssays(BioAssay bioAssay)
Method to remove first BioAssay from BioAssays_list

Specified by:
removeFromBioAssays in interface HasBioAssays

setExperimentDesigns

public void setExperimentDesigns(HasExperimentDesigns.ExperimentDesigns_list experimentDesigns)
Set method for experimentDesigns

Specified by:
setExperimentDesigns in interface HasExperimentDesigns
Parameters:
value - to set

getExperimentDesigns

public HasExperimentDesigns.ExperimentDesigns_list getExperimentDesigns()
Get method for experimentDesigns

Specified by:
getExperimentDesigns in interface HasExperimentDesigns
Returns:
value of the attribute

addToExperimentDesigns

public void addToExperimentDesigns(ExperimentDesign experimentDesign)
Method to add ExperimentDesign to ExperimentDesigns_list

Specified by:
addToExperimentDesigns in interface HasExperimentDesigns

addToExperimentDesigns

public void addToExperimentDesigns(int position,
                                   ExperimentDesign experimentDesign)
Method to add ExperimentDesign at position to ExperimentDesigns_list

Specified by:
addToExperimentDesigns in interface HasExperimentDesigns

getFromExperimentDesigns

public ExperimentDesign getFromExperimentDesigns(int position)
Method to get ExperimentDesign from ExperimentDesigns_list

Specified by:
getFromExperimentDesigns in interface HasExperimentDesigns

removeElementAtFromExperimentDesigns

public void removeElementAtFromExperimentDesigns(int position)
Method to remove by position from ExperimentDesigns_list

Specified by:
removeElementAtFromExperimentDesigns in interface HasExperimentDesigns

removeFromExperimentDesigns

public void removeFromExperimentDesigns(ExperimentDesign experimentDesign)
Method to remove first ExperimentDesign from ExperimentDesigns_list

Specified by:
removeFromExperimentDesigns in interface HasExperimentDesigns

isDeleted

public boolean isDeleted()
Returns:
- True if this Experiment is deleted; false otherwise.

setDeleted

public void setDeleted(boolean deleted)
Sets if this Experiment is deleted.

Parameters:
deleted - - True if this Experiment is deleted; false otherwise.