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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.Experiment.Experiment
public class Experiment
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasAnalysisResults |
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HasAnalysisResults.AnalysisResults_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssays |
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HasBioAssays.BioAssays_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProviders |
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HasProviders.Providers_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayData |
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HasBioAssayData.BioAssayData_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasExperimentDesigns |
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HasExperimentDesigns.ExperimentDesigns_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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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 |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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Experiment()
Default constructor. |
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Experiment(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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)
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Contact |
getFromProviders(int position)
Method to get Contact from Providers_list |
java.lang.String |
getModelClassName()
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java.util.ArrayList |
getProviderRoles()
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HasProviders.Providers_list |
getProviders()
Get method for providers |
boolean |
isDeleted()
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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)
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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)
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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 |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected java.util.List providerRoles
protected java.util.List analysisResults
protected java.util.List bioAssayData
protected java.util.List bioAssays
protected java.util.List experimentDesigns
protected boolean deleted
Constructor Detail |
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public Experiment()
public Experiment(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setProviders(HasProviders.Providers_list providers)
setProviders
in interface HasProviders
value
- to setpublic void setProviderRoles(java.util.ArrayList providerRoles)
providerRoles
- public HasProviders.Providers_list getProviders()
getProviders
in interface HasProviders
public java.util.ArrayList getProviderRoles()
public void addToProviders(Contact contact)
addToProviders
in interface HasProviders
public void addToProviderRoles(ExperimentProviderRole providerRole)
providerRole
- - A provider who has a role such as investigator,
primary contact, etc.public void addToProviders(int position, Contact contact)
addToProviders
in interface HasProviders
public void addToProviderRoles(int position, ExperimentProviderRole providerRole)
public Contact getFromProviders(int position)
getFromProviders
in interface HasProviders
public ExperimentProviderRole getFromProviderRoles(int position)
public void removeElementAtFromProviders(int position)
removeElementAtFromProviders
in interface HasProviders
public void removeFromProviders(Contact contact)
removeFromProviders
in interface HasProviders
public void removeFromProviderRoles(ExperimentProviderRole providerRole)
public void setAnalysisResults(HasAnalysisResults.AnalysisResults_list analysisResults)
setAnalysisResults
in interface HasAnalysisResults
value
- to setpublic HasAnalysisResults.AnalysisResults_list getAnalysisResults()
getAnalysisResults
in interface HasAnalysisResults
public void addToAnalysisResults(BioAssayDataCluster bioAssayDataCluster)
addToAnalysisResults
in interface HasAnalysisResults
public void addToAnalysisResults(int position, BioAssayDataCluster bioAssayDataCluster)
addToAnalysisResults
in interface HasAnalysisResults
public BioAssayDataCluster getFromAnalysisResults(int position)
getFromAnalysisResults
in interface HasAnalysisResults
public void removeElementAtFromAnalysisResults(int position)
removeElementAtFromAnalysisResults
in interface HasAnalysisResults
public void removeFromAnalysisResults(BioAssayDataCluster bioAssayDataCluster)
removeFromAnalysisResults
in interface HasAnalysisResults
public void setBioAssayData(HasBioAssayData.BioAssayData_list bioAssayData)
setBioAssayData
in interface HasBioAssayData
value
- to setpublic HasBioAssayData.BioAssayData_list getBioAssayData()
getBioAssayData
in interface HasBioAssayData
public void addToBioAssayData(BioAssayData bioAssayData)
addToBioAssayData
in interface HasBioAssayData
public void addToBioAssayData(int position, BioAssayData bioAssayData)
addToBioAssayData
in interface HasBioAssayData
public BioAssayData getFromBioAssayData(int position)
getFromBioAssayData
in interface HasBioAssayData
public void removeElementAtFromBioAssayData(int position)
removeElementAtFromBioAssayData
in interface HasBioAssayData
public void removeFromBioAssayData(BioAssayData bioAssayData)
removeFromBioAssayData
in interface HasBioAssayData
public void setBioAssays(HasBioAssays.BioAssays_list bioAssays)
setBioAssays
in interface HasBioAssays
value
- to setpublic HasBioAssays.BioAssays_list getBioAssays()
getBioAssays
in interface HasBioAssays
public void addToBioAssays(BioAssay bioAssay)
addToBioAssays
in interface HasBioAssays
public void addToBioAssays(int position, BioAssay bioAssay)
addToBioAssays
in interface HasBioAssays
public BioAssay getFromBioAssays(int position)
getFromBioAssays
in interface HasBioAssays
public void removeElementAtFromBioAssays(int position)
removeElementAtFromBioAssays
in interface HasBioAssays
public void removeFromBioAssays(BioAssay bioAssay)
removeFromBioAssays
in interface HasBioAssays
public void setExperimentDesigns(HasExperimentDesigns.ExperimentDesigns_list experimentDesigns)
setExperimentDesigns
in interface HasExperimentDesigns
value
- to setpublic HasExperimentDesigns.ExperimentDesigns_list getExperimentDesigns()
getExperimentDesigns
in interface HasExperimentDesigns
public void addToExperimentDesigns(ExperimentDesign experimentDesign)
addToExperimentDesigns
in interface HasExperimentDesigns
public void addToExperimentDesigns(int position, ExperimentDesign experimentDesign)
addToExperimentDesigns
in interface HasExperimentDesigns
public ExperimentDesign getFromExperimentDesigns(int position)
getFromExperimentDesigns
in interface HasExperimentDesigns
public void removeElementAtFromExperimentDesigns(int position)
removeElementAtFromExperimentDesigns
in interface HasExperimentDesigns
public void removeFromExperimentDesigns(ExperimentDesign experimentDesign)
removeFromExperimentDesigns
in interface HasExperimentDesigns
public boolean isDeleted()
public void setDeleted(boolean deleted)
deleted
- - True if this Experiment is deleted; false otherwise.
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