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SUMMARY: JavaDoc of org.biomage.Experiment.Experiment JAVADOC | Sourc code of org.biomage.Experiment.Experiment SOURCE | Download org.biomage.Experiment.Experiment DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

org.biomage.Experiment
Class Experiment  view Experiment download Experiment.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.Experiment.Experiment
All Implemented Interfaces:
org.biomage.Interface.HasAnalysisResults, org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayData, org.biomage.Interface.HasBioAssays, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasExperimentDesign, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProviders, org.biomage.Interface.HasSecurity, java.io.Serializable
public class Experiment
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasAnalysisResults, org.biomage.Interface.HasBioAssays, org.biomage.Interface.HasProviders, org.biomage.Interface.HasBioAssayData, org.biomage.Interface.HasExperimentDesign

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

Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasAnalysisResults
org.biomage.Interface.HasAnalysisResults.AnalysisResults_list
 
Nested classes inherited from class org.biomage.Interface.HasBioAssays
org.biomage.Interface.HasBioAssays.BioAssays_list
 
Nested classes inherited from class org.biomage.Interface.HasProviders
org.biomage.Interface.HasProviders.Providers_list
 
Nested classes inherited from class org.biomage.Interface.HasBioAssayData
org.biomage.Interface.HasBioAssayData.BioAssayData_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.Interface.HasAnalysisResults.AnalysisResults_list analysisResults
          The results of analyzing the data, typically with a clustering algorithm.
private  org.biomage.Interface.HasBioAssayData.BioAssayData_list bioAssayData
          The collection of BioAssayDatas for this Experiment.
private  org.biomage.Interface.HasBioAssays.BioAssays_list bioAssays
          The collection of BioAssays for this Experiment.
private  ExperimentDesign experimentDesign
          The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.
private  org.biomage.Interface.HasProviders.Providers_list providers
          The providers of the Experiment, its data and annotation.
 
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
Experiment()
          Default constructor.
Experiment(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToAnalysisResults(org.biomage.HigherLevelAnalysis.BioAssayDataCluster bioAssayDataCluster)
          Method to add BioAssayDataCluster to AnalysisResults_list
 void addToAnalysisResults(int position, org.biomage.HigherLevelAnalysis.BioAssayDataCluster bioAssayDataCluster)
          Method to add BioAssayDataCluster at position to AnalysisResults_list
 void addToBioAssayData(org.biomage.BioAssayData.BioAssayData bioAssayData)
          Method to add BioAssayData to BioAssayData_list
 void addToBioAssayData(int position, org.biomage.BioAssayData.BioAssayData bioAssayData)
          Method to add BioAssayData at position to BioAssayData_list
 void addToBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
          Method to add BioAssay to BioAssays_list
 void addToBioAssays(int position, org.biomage.BioAssay.BioAssay bioAssay)
          Method to add BioAssay at position to BioAssays_list
 void addToProviders(org.biomage.AuditAndSecurity.Contact contact)
          Method to add Contact to Providers_list
 void addToProviders(int position, org.biomage.AuditAndSecurity.Contact contact)
          Method to add Contact at position to Providers_list
 org.biomage.Interface.HasAnalysisResults.AnalysisResults_list getAnalysisResults()
          Get method for analysisResults
 org.biomage.Interface.HasBioAssayData.BioAssayData_list getBioAssayData()
          Get method for bioAssayData
 org.biomage.Interface.HasBioAssays.BioAssays_list getBioAssays()
          Get method for bioAssays
 ExperimentDesign getExperimentDesign()
          Get method for experimentDesign
 org.biomage.HigherLevelAnalysis.BioAssayDataCluster getFromAnalysisResults(int position)
          Method to get BioAssayDataCluster from AnalysisResults_list
 org.biomage.BioAssayData.BioAssayData getFromBioAssayData(int position)
          Method to get BioAssayData from BioAssayData_list
 org.biomage.BioAssay.BioAssay getFromBioAssays(int position)
          Method to get BioAssay from BioAssays_list
 org.biomage.AuditAndSecurity.Contact getFromProviders(int position)
          Method to get Contact from Providers_list
 org.biomage.Interface.HasProviders.Providers_list getProviders()
          Get method for providers
 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 removeElementAtFromProviders(int position)
          Method to remove by position from Providers_list
 void removeFromAnalysisResults(org.biomage.HigherLevelAnalysis.BioAssayDataCluster bioAssayDataCluster)
          Method to remove first BioAssayDataCluster from AnalysisResults_list
 void removeFromBioAssayData(org.biomage.BioAssayData.BioAssayData bioAssayData)
          Method to remove first BioAssayData from BioAssayData_list
 void removeFromBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
          Method to remove first BioAssay from BioAssays_list
 void removeFromProviders(org.biomage.AuditAndSecurity.Contact contact)
          Method to remove first Contact from Providers_list
 void setAnalysisResults(org.biomage.Interface.HasAnalysisResults.AnalysisResults_list analysisResults)
          Set method for analysisResults
 void setBioAssayData(org.biomage.Interface.HasBioAssayData.BioAssayData_list bioAssayData)
          Set method for bioAssayData
 void setBioAssays(org.biomage.Interface.HasBioAssays.BioAssays_list bioAssays)
          Set method for bioAssays
 void setExperimentDesign(ExperimentDesign experimentDesign)
          Set method for experimentDesign
 void setProviders(org.biomage.Interface.HasProviders.Providers_list providers)
          Set method for providers
 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

analysisResults

private org.biomage.Interface.HasAnalysisResults.AnalysisResults_list analysisResults
The results of analyzing the data, typically with a clustering algorithm.

bioAssays

private org.biomage.Interface.HasBioAssays.BioAssays_list bioAssays
The collection of BioAssays for this Experiment.

providers

private org.biomage.Interface.HasProviders.Providers_list providers
The providers of the Experiment, its data and annotation.

bioAssayData

private org.biomage.Interface.HasBioAssayData.BioAssayData_list bioAssayData
The collection of BioAssayDatas for this Experiment.

experimentDesign

private ExperimentDesign experimentDesign
The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.

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

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.

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.

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.

setAnalysisResults

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

Specified by:
setAnalysisResults in interface org.biomage.Interface.HasAnalysisResults

getAnalysisResults

public org.biomage.Interface.HasAnalysisResults.AnalysisResults_list getAnalysisResults()
Get method for analysisResults

Specified by:
getAnalysisResults in interface org.biomage.Interface.HasAnalysisResults

addToAnalysisResults

public void addToAnalysisResults(org.biomage.HigherLevelAnalysis.BioAssayDataCluster bioAssayDataCluster)
Method to add BioAssayDataCluster to AnalysisResults_list

Specified by:
addToAnalysisResults in interface org.biomage.Interface.HasAnalysisResults

addToAnalysisResults

public void addToAnalysisResults(int position,
                                 org.biomage.HigherLevelAnalysis.BioAssayDataCluster bioAssayDataCluster)
Method to add BioAssayDataCluster at position to AnalysisResults_list

Specified by:
addToAnalysisResults in interface org.biomage.Interface.HasAnalysisResults

getFromAnalysisResults

public org.biomage.HigherLevelAnalysis.BioAssayDataCluster getFromAnalysisResults(int position)
Method to get BioAssayDataCluster from AnalysisResults_list

Specified by:
getFromAnalysisResults in interface org.biomage.Interface.HasAnalysisResults

removeElementAtFromAnalysisResults

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

Specified by:
removeElementAtFromAnalysisResults in interface org.biomage.Interface.HasAnalysisResults

removeFromAnalysisResults

public void removeFromAnalysisResults(org.biomage.HigherLevelAnalysis.BioAssayDataCluster bioAssayDataCluster)
Method to remove first BioAssayDataCluster from AnalysisResults_list

Specified by:
removeFromAnalysisResults in interface org.biomage.Interface.HasAnalysisResults

setBioAssays

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

Specified by:
setBioAssays in interface org.biomage.Interface.HasBioAssays

getBioAssays

public org.biomage.Interface.HasBioAssays.BioAssays_list getBioAssays()
Get method for bioAssays

Specified by:
getBioAssays in interface org.biomage.Interface.HasBioAssays

addToBioAssays

public void addToBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
Method to add BioAssay to BioAssays_list

Specified by:
addToBioAssays in interface org.biomage.Interface.HasBioAssays

addToBioAssays

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

Specified by:
addToBioAssays in interface org.biomage.Interface.HasBioAssays

getFromBioAssays

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

Specified by:
getFromBioAssays in interface org.biomage.Interface.HasBioAssays

removeElementAtFromBioAssays

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

Specified by:
removeElementAtFromBioAssays in interface org.biomage.Interface.HasBioAssays

removeFromBioAssays

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

Specified by:
removeFromBioAssays in interface org.biomage.Interface.HasBioAssays

setProviders

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

Specified by:
setProviders in interface org.biomage.Interface.HasProviders

getProviders

public org.biomage.Interface.HasProviders.Providers_list getProviders()
Get method for providers

Specified by:
getProviders in interface org.biomage.Interface.HasProviders

addToProviders

public void addToProviders(org.biomage.AuditAndSecurity.Contact contact)
Method to add Contact to Providers_list

Specified by:
addToProviders in interface org.biomage.Interface.HasProviders

addToProviders

public void addToProviders(int position,
                           org.biomage.AuditAndSecurity.Contact contact)
Method to add Contact at position to Providers_list

Specified by:
addToProviders in interface org.biomage.Interface.HasProviders

getFromProviders

public org.biomage.AuditAndSecurity.Contact getFromProviders(int position)
Method to get Contact from Providers_list

Specified by:
getFromProviders in interface org.biomage.Interface.HasProviders

removeElementAtFromProviders

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

Specified by:
removeElementAtFromProviders in interface org.biomage.Interface.HasProviders

removeFromProviders

public void removeFromProviders(org.biomage.AuditAndSecurity.Contact contact)
Method to remove first Contact from Providers_list

Specified by:
removeFromProviders in interface org.biomage.Interface.HasProviders

setBioAssayData

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

Specified by:
setBioAssayData in interface org.biomage.Interface.HasBioAssayData

getBioAssayData

public org.biomage.Interface.HasBioAssayData.BioAssayData_list getBioAssayData()
Get method for bioAssayData

Specified by:
getBioAssayData in interface org.biomage.Interface.HasBioAssayData

addToBioAssayData

public void addToBioAssayData(org.biomage.BioAssayData.BioAssayData bioAssayData)
Method to add BioAssayData to BioAssayData_list

Specified by:
addToBioAssayData in interface org.biomage.Interface.HasBioAssayData

addToBioAssayData

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

Specified by:
addToBioAssayData in interface org.biomage.Interface.HasBioAssayData

getFromBioAssayData

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

Specified by:
getFromBioAssayData in interface org.biomage.Interface.HasBioAssayData

removeElementAtFromBioAssayData

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

Specified by:
removeElementAtFromBioAssayData in interface org.biomage.Interface.HasBioAssayData

removeFromBioAssayData

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

Specified by:
removeFromBioAssayData in interface org.biomage.Interface.HasBioAssayData

setExperimentDesign

public void setExperimentDesign(ExperimentDesign experimentDesign)
Set method for experimentDesign

Specified by:
setExperimentDesign in interface org.biomage.Interface.HasExperimentDesign

getExperimentDesign

public ExperimentDesign getExperimentDesign()
Get method for experimentDesign

Specified by:
getExperimentDesign in interface org.biomage.Interface.HasExperimentDesign
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SUMMARY: JavaDoc of org.biomage.Experiment.Experiment JAVADOC | Sourc code of org.biomage.Experiment.Experiment SOURCE | Download org.biomage.Experiment.Experiment DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD