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A
- addToAnalysisResults(BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment
- Method to add BioAssayDataCluster to AnalysisResults_list
- addToAnalysisResults(int, BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment
- Method to add BioAssayDataCluster at position to AnalysisResults_list
- addToBioAssayData(BioAssayData) - Method in class org.biomage.Experiment.Experiment
- Method to add BioAssayData to BioAssayData_list
- addToBioAssayData(int, BioAssayData) - Method in class org.biomage.Experiment.Experiment
- Method to add BioAssayData at position to BioAssayData_list
- addToBioAssays(BioAssay) - Method in class org.biomage.Experiment.Experiment
- Method to add BioAssay to BioAssays_list
- addToBioAssays(int, BioAssay) - Method in class org.biomage.Experiment.Experiment
- Method to add BioAssay at position to BioAssays_list
- addToExperiment_list(Experiment) - Method in class org.biomage.Experiment.Experiment_package
- Method to add Experiment to Experiment_list
- addToExperiment_list(int, Experiment) - Method in class org.biomage.Experiment.Experiment_package
- Method to add Experiment at position to Experiment_list
- addToExperimentalFactors(ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to add ExperimentalFactor to ExperimentalFactors_list
- addToExperimentalFactors(int, ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to add ExperimentalFactor at position to ExperimentalFactors_list
- addToFactorValues(FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor
- Method to add FactorValue to FactorValues_list
- addToFactorValues(int, FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor
- Method to add FactorValue at position to FactorValues_list
- addToProviders(Contact) - Method in class org.biomage.Experiment.Experiment
- Method to add Contact to Providers_list
- addToProviders(int, Contact) - Method in class org.biomage.Experiment.Experiment
- Method to add Contact at position to Providers_list
- addToTopLevelBioAssays(BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to add BioAssay to TopLevelBioAssays_list
- addToTopLevelBioAssays(int, BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to add BioAssay at position to TopLevelBioAssays_list
- addToTypes(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to add OntologyEntry to Types_list
- addToTypes(int, OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to add OntologyEntry at position to Types_list
- analysisResults - Variable in class org.biomage.Experiment.Experiment
- The results of analyzing the data, typically with a clustering algorithm.
B
- bioAssayData - Variable in class org.biomage.Experiment.Experiment
- The collection of BioAssayDatas for this Experiment.
- bioAssays - Variable in class org.biomage.Experiment.Experiment
- The collection of BioAssays for this Experiment.
C
- category - Variable in class org.biomage.Experiment.ExperimentalFactor
- The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).
E
- Experiment - class org.biomage.Experiment.Experiment.
- The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
- Experiment() - Constructor for class org.biomage.Experiment.Experiment
- Default constructor.
- Experiment(Attributes) - Constructor for class org.biomage.Experiment.Experiment
- Attribute constructor.
- ExperimentDesign - class org.biomage.Experiment.ExperimentDesign.
- The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.
- ExperimentDesign() - Constructor for class org.biomage.Experiment.ExperimentDesign
- Default constructor.
- ExperimentDesign(Attributes) - Constructor for class org.biomage.Experiment.ExperimentDesign
- Attribute constructor.
- Experiment_package - class org.biomage.Experiment.Experiment_package.
- Represents the container for a hierarchical grouping of BioAssays.
- Experiment_package() - Constructor for class org.biomage.Experiment.Experiment_package
- Default constructor.
- Experiment_package(Attributes) - Constructor for class org.biomage.Experiment.Experiment_package
- Attribute constructor.
- Experiment_package.Experiment_list - class org.biomage.Experiment.Experiment_package.Experiment_list.
- Inner list class for holding multiple entries for attribute experiment_list.
- Experiment_package.Experiment_list() - Constructor for class org.biomage.Experiment.Experiment_package.Experiment_list
- ExperimentalFactor - class org.biomage.Experiment.ExperimentalFactor.
- ExperimentFactors are the dependent variables of an experiment (e.g.
- ExperimentalFactor() - Constructor for class org.biomage.Experiment.ExperimentalFactor
- Default constructor.
- ExperimentalFactor(Attributes) - Constructor for class org.biomage.Experiment.ExperimentalFactor
- Attribute constructor.
- experimentDesign - Variable in class org.biomage.Experiment.Experiment
- The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.
- experiment_list - Variable in class org.biomage.Experiment.Experiment_package
- The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
- experimentalFactor - Variable in class org.biomage.Experiment.FactorValue
- The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.
- experimentalFactors - Variable in class org.biomage.Experiment.ExperimentDesign
- The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays.
F
- FactorValue - class org.biomage.Experiment.FactorValue.
- The value for a ExperimentalFactor
- FactorValue() - Constructor for class org.biomage.Experiment.FactorValue
- Default constructor.
- FactorValue(Attributes) - Constructor for class org.biomage.Experiment.FactorValue
- Attribute constructor.
- factorValues - Variable in class org.biomage.Experiment.ExperimentalFactor
- The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.
G
- getAnalysisResults() - Method in class org.biomage.Experiment.Experiment
- Get method for analysisResults
- getBioAssayData() - Method in class org.biomage.Experiment.Experiment
- Get method for bioAssayData
- getBioAssays() - Method in class org.biomage.Experiment.Experiment
- Get method for bioAssays
- getCategory() - Method in class org.biomage.Experiment.ExperimentalFactor
- Get method for category
- getExperimentDesign() - Method in class org.biomage.Experiment.Experiment
- Get method for experimentDesign
- getExperiment_list() - Method in class org.biomage.Experiment.Experiment_package
- Get method for experiment_list
- getExperimentalFactor() - Method in class org.biomage.Experiment.FactorValue
- Get method for experimentalFactor
- getExperimentalFactors() - Method in class org.biomage.Experiment.ExperimentDesign
- Get method for experimentalFactors
- getFactorValues() - Method in class org.biomage.Experiment.ExperimentalFactor
- Get method for factorValues
- getFromAnalysisResults(int) - Method in class org.biomage.Experiment.Experiment
- Method to get BioAssayDataCluster from AnalysisResults_list
- getFromBioAssayData(int) - Method in class org.biomage.Experiment.Experiment
- Method to get BioAssayData from BioAssayData_list
- getFromBioAssays(int) - Method in class org.biomage.Experiment.Experiment
- Method to get BioAssay from BioAssays_list
- getFromExperiment_list(int) - Method in class org.biomage.Experiment.Experiment_package
- Method to get Experiment from Experiment_list
- getFromExperimentalFactors(int) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to get ExperimentalFactor from ExperimentalFactors_list
- getFromFactorValues(int) - Method in class org.biomage.Experiment.ExperimentalFactor
- Method to get FactorValue from FactorValues_list
- getFromProviders(int) - Method in class org.biomage.Experiment.Experiment
- Method to get Contact from Providers_list
- getFromTopLevelBioAssays(int) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to get BioAssay from TopLevelBioAssays_list
- getFromTypes(int) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to get OntologyEntry from Types_list
- getMeasurement() - Method in class org.biomage.Experiment.FactorValue
- Get method for measurement
- getNormalizationDescription() - Method in class org.biomage.Experiment.ExperimentDesign
- Get method for normalizationDescription
- getProviders() - Method in class org.biomage.Experiment.Experiment
- Get method for providers
- getQualityControlDescription() - Method in class org.biomage.Experiment.ExperimentDesign
- Get method for qualityControlDescription
- getReplicateDescription() - Method in class org.biomage.Experiment.ExperimentDesign
- Get method for replicateDescription
- getTopLevelBioAssays() - Method in class org.biomage.Experiment.ExperimentDesign
- Get method for topLevelBioAssays
- getTypes() - Method in class org.biomage.Experiment.ExperimentDesign
- Get method for types
M
- measurement - Variable in class org.biomage.Experiment.FactorValue
- The measured value for this factor.
N
- normalizationDescription - Variable in class org.biomage.Experiment.ExperimentDesign
- Description of the normalization strategy of the Experiment.
O
- org.biomage.Experiment - package org.biomage.Experiment
P
- providers - Variable in class org.biomage.Experiment.Experiment
- The providers of the Experiment, its data and annotation.
Q
- qualityControlDescription - Variable in class org.biomage.Experiment.ExperimentDesign
- Description of the quality control aspects of the Experiment.
R
- removeElementAtFromAnalysisResults(int) - Method in class org.biomage.Experiment.Experiment
- Method to remove by position from AnalysisResults_list
- removeElementAtFromBioAssayData(int) - Method in class org.biomage.Experiment.Experiment
- Method to remove by position from BioAssayData_list
- removeElementAtFromBioAssays(int) - Method in class org.biomage.Experiment.Experiment
- Method to remove by position from BioAssays_list
- removeElementAtFromExperiment_list(int) - Method in class org.biomage.Experiment.Experiment_package
- Method to remove by position from Experiment_list
- removeElementAtFromExperimentalFactors(int) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to remove by position from ExperimentalFactors_list
- removeElementAtFromFactorValues(int) - Method in class org.biomage.Experiment.ExperimentalFactor
- Method to remove by position from FactorValues_list
- removeElementAtFromProviders(int) - Method in class org.biomage.Experiment.Experiment
- Method to remove by position from Providers_list
- removeElementAtFromTopLevelBioAssays(int) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to remove by position from TopLevelBioAssays_list
- removeElementAtFromTypes(int) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to remove by position from Types_list
- removeFromAnalysisResults(BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment
- Method to remove first BioAssayDataCluster from AnalysisResults_list
- removeFromBioAssayData(BioAssayData) - Method in class org.biomage.Experiment.Experiment
- Method to remove first BioAssayData from BioAssayData_list
- removeFromBioAssays(BioAssay) - Method in class org.biomage.Experiment.Experiment
- Method to remove first BioAssay from BioAssays_list
- removeFromExperiment_list(Experiment) - Method in class org.biomage.Experiment.Experiment_package
- Method to remove first Experiment from Experiment_list
- removeFromExperimentalFactors(ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to remove first ExperimentalFactor from ExperimentalFactors_list
- removeFromFactorValues(FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor
- Method to remove first FactorValue from FactorValues_list
- removeFromProviders(Contact) - Method in class org.biomage.Experiment.Experiment
- Method to remove first Contact from Providers_list
- removeFromTopLevelBioAssays(BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to remove first BioAssay from TopLevelBioAssays_list
- removeFromTypes(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign
- Method to remove first OntologyEntry from Types_list
- replicateDescription - Variable in class org.biomage.Experiment.ExperimentDesign
- Description of the replicate strategy of the Experiment.
S
- setAnalysisResults(HasAnalysisResults.AnalysisResults_list) - Method in class org.biomage.Experiment.Experiment
- Set method for analysisResults
- setBioAssayData(HasBioAssayData.BioAssayData_list) - Method in class org.biomage.Experiment.Experiment
- Set method for bioAssayData
- setBioAssays(HasBioAssays.BioAssays_list) - Method in class org.biomage.Experiment.Experiment
- Set method for bioAssays
- setCategory(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentalFactor
- Set method for category
- setExperimentDesign(ExperimentDesign) - Method in class org.biomage.Experiment.Experiment
- Set method for experimentDesign
- setExperiment_list(Experiment_package.Experiment_list) - Method in class org.biomage.Experiment.Experiment_package
- Set method for experiment_list
- setExperimentalFactor(ExperimentalFactor) - Method in class org.biomage.Experiment.FactorValue
- Set method for experimentalFactor
- setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list) - Method in class org.biomage.Experiment.ExperimentDesign
- Set method for experimentalFactors
- setFactorValues(HasFactorValues.FactorValues_list) - Method in class org.biomage.Experiment.ExperimentalFactor
- Set method for factorValues
- setMeasurement(Measurement) - Method in class org.biomage.Experiment.FactorValue
- Set method for measurement
- setNormalizationDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign
- Set method for normalizationDescription
- setProviders(HasProviders.Providers_list) - Method in class org.biomage.Experiment.Experiment
- Set method for providers
- setQualityControlDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign
- Set method for qualityControlDescription
- setReplicateDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign
- Set method for replicateDescription
- setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list) - Method in class org.biomage.Experiment.ExperimentDesign
- Set method for topLevelBioAssays
- setTypes(HasTypes.Types_list) - Method in class org.biomage.Experiment.ExperimentDesign
- Set method for types
T
- topLevelBioAssays - Variable in class org.biomage.Experiment.ExperimentDesign
- The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)
- types - Variable in class org.biomage.Experiment.ExperimentDesign
- Classification of an experiment.
W
- writeAssociations(Writer) - Method in class org.biomage.Experiment.Experiment
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Experiment.ExperimentDesign
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Experiment.Experiment_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Experiment.ExperimentalFactor
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Experiment.FactorValue
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.Experiment.Experiment
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Experiment.ExperimentDesign
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Experiment.Experiment_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Experiment.ExperimentalFactor
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Experiment.FactorValue
- writeAttributes
- writeMAGEML(Writer) - Method in class org.biomage.Experiment.Experiment
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Experiment.ExperimentDesign
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Experiment.Experiment_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Experiment.ExperimentalFactor
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Experiment.FactorValue
- writeMAGEML
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