Uses of Interface
gov.nih.nci.mageom.domain.Identifiable

Packages that use Identifiable
gov.nih.nci.mageom.domain.Array   
gov.nih.nci.mageom.domain.Array.impl   
gov.nih.nci.mageom.domain.ArrayDesign   
gov.nih.nci.mageom.domain.ArrayDesign.impl   
gov.nih.nci.mageom.domain.AuditAndSecurity   
gov.nih.nci.mageom.domain.AuditAndSecurity.impl   
gov.nih.nci.mageom.domain.BioAssay   
gov.nih.nci.mageom.domain.BioAssay.impl   
gov.nih.nci.mageom.domain.BioAssayData   
gov.nih.nci.mageom.domain.BioAssayData.impl   
gov.nih.nci.mageom.domain.BioEvent   
gov.nih.nci.mageom.domain.BioEvent.impl   
gov.nih.nci.mageom.domain.BioMaterial   
gov.nih.nci.mageom.domain.BioMaterial.impl   
gov.nih.nci.mageom.domain.BioSequence   
gov.nih.nci.mageom.domain.BioSequence.impl   
gov.nih.nci.mageom.domain.Description   
gov.nih.nci.mageom.domain.Description.impl   
gov.nih.nci.mageom.domain.DesignElement   
gov.nih.nci.mageom.domain.DesignElement.impl   
gov.nih.nci.mageom.domain.Experiment   
gov.nih.nci.mageom.domain.Experiment.impl   
gov.nih.nci.mageom.domain.HigherLevelAnalysis   
gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl   
gov.nih.nci.mageom.domain.impl   
gov.nih.nci.mageom.domain.Protocol   
gov.nih.nci.mageom.domain.Protocol.impl   
gov.nih.nci.mageom.domain.QuantitationType   
gov.nih.nci.mageom.domain.QuantitationType.impl   
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Array
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Array
 interface Array
          The physical substrate along with its features and their annotation
 interface ArrayGroup
          An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
 interface ArrayManufacture
          Describes the process by which arrays are produced.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Array.impl
 

Classes in gov.nih.nci.mageom.domain.Array.impl that implement Identifiable
 class ArrayGroupImpl
          An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
 class ArrayImpl
          The physical substrate along with its features and their annotation
 class ArrayManufactureImpl
          Describes the process by which arrays are produced.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.ArrayDesign
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.ArrayDesign
 interface ArrayDesign
          Describes the design of an gene expression layout.
 interface CompositeGroup
          Allows specification of the type of Composite Design Element.
 interface DesignElementGroup
          The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
 interface FeatureGroup
          A collection of like features.
 interface PhysicalArrayDesign
          A design that is expected to be used to manufacture physical arrays.
 interface ReporterGroup
          Allows specification of the type of Reporter Design Element.
 interface Zone
          Specifies the location of a zone on an array.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.ArrayDesign.impl
 

Classes in gov.nih.nci.mageom.domain.ArrayDesign.impl that implement Identifiable
 class ArrayDesignImpl
          Describes the design of an gene expression layout.
 class CompositeGroupImpl
          Allows specification of the type of Composite Design Element.
 class DesignElementGroupImpl
          The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
 class FeatureGroupImpl
          A collection of like features.
 class PhysicalArrayDesignImpl
          A design that is expected to be used to manufacture physical arrays.
 class ReporterGroupImpl
          Allows specification of the type of Reporter Design Element.
 class ZoneImpl
          Specifies the location of a zone on an array.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.AuditAndSecurity
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.AuditAndSecurity
 interface Contact
          A contact is either a person or an organization.
 interface Organization
          Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
 interface Person
          A person for which the attributes are self describing.
 interface Security
          Permission information for an object as to ownership, write and read permissions.
 interface SecurityGroup
          Groups contacts together based on their security privileges.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.AuditAndSecurity.impl
 

Classes in gov.nih.nci.mageom.domain.AuditAndSecurity.impl that implement Identifiable
 class ContactImpl
          A contact is either a person or an organization.
 class OrganizationImpl
          Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
 class PersonImpl
          A person for which the attributes are self describing.
 class SecurityGroupImpl
          Groups contacts together based on their security privileges.
 class SecurityImpl
          Permission information for an object as to ownership, write and read permissions.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssay
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioAssay
 interface BioAssay
          An abstract class which represents both physical and computational groupings of arrays and biomaterials.
 interface BioAssayCreation
          The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.
 interface BioAssayTreatment
          The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).
 interface Channel
          A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
 interface DerivedBioAssay
          A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
 interface FeatureExtraction
          The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay.
 interface Hybridization
          The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array.
 interface Image
          An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay).
 interface ImageAcquisition
          The process by which an image is generated (typically scanning).
 interface MeasuredBioAssay
          A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
 interface PhysicalBioAssay
          A bioAssay created by the bioAssayCreation event (e.g.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssay.impl
 

Classes in gov.nih.nci.mageom.domain.BioAssay.impl that implement Identifiable
 class BioAssayCreationImpl
          The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.
 class BioAssayImpl
          An abstract class which represents both physical and computational groupings of arrays and biomaterials.
 class BioAssayTreatmentImpl
          The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).
 class ChannelImpl
          A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
 class DerivedBioAssayImpl
          A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
 class FeatureExtractionImpl
          The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay.
 class HybridizationImpl
          The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array.
 class ImageAcquisitionImpl
          The process by which an image is generated (typically scanning).
 class ImageImpl
          An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay).
 class MeasuredBioAssayImpl
          A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
 class PhysicalBioAssayImpl
          A bioAssay created by the bioAssayCreation event (e.g.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssayData
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioAssayData
 interface BioAssayData
          Represents the dataset created when the BioAssays are created.
 interface BioAssayDimension
          An ordered list of bioAssays.
 interface BioAssayMap
          The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
 interface CompositeSequenceDimension
          Specialized DesignElementDimension to hold CompositeSequences.
 interface DerivedBioAssayData
          The output of a transformation event.
 interface DesignElementDimension
          An ordered list of designElements.
 interface DesignElementMap
          A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
 interface FeatureDimension
          Specialized DesignElementDimension to hold Features.
 interface MeasuredBioAssayData
          The data associated with the MeasuredBioAssay produced by FeatureExtraction.
 interface QuantitationTypeDimension
          An ordered list of quantitationTypes.
 interface QuantitationTypeMap
          A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
 interface ReporterDimension
          Specialized DesignElementDimension to hold Reporters.
 interface Transformation
          The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssayData.impl
 

Classes in gov.nih.nci.mageom.domain.BioAssayData.impl that implement Identifiable
 class BioAssayDataImpl
          Represents the dataset created when the BioAssays are created.
 class BioAssayDimensionImpl
          An ordered list of bioAssays.
 class BioAssayMapImpl
          The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
 class CompositeSequenceDimensionImpl
          Specialized DesignElementDimension to hold CompositeSequences.
 class DerivedBioAssayDataImpl
          The output of a transformation event.
 class DesignElementDimensionImpl
          An ordered list of designElements.
 class DesignElementMapImpl
          A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
 class FeatureDimensionImpl
          Specialized DesignElementDimension to hold Features.
 class MeasuredBioAssayDataImpl
          The data associated with the MeasuredBioAssay produced by FeatureExtraction.
 class QuantitationTypeDimensionImpl
          An ordered list of quantitationTypes.
 class QuantitationTypeMapImpl
          A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
 class ReporterDimensionImpl
          Specialized DesignElementDimension to hold Reporters.
 class TransformationImpl
          The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioEvent
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioEvent
 interface BioEvent
          An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
 interface Map
          A Map is the description of how sources are transformed into a target.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioEvent.impl
 

Classes in gov.nih.nci.mageom.domain.BioEvent.impl that implement Identifiable
 class BioEventImpl
          An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
 class MapImpl
          A Map is the description of how sources are transformed into a target.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioMaterial
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioMaterial
 interface BioMaterial
          BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
 interface BioSample
          BioSamples are products of treatments that are of interest.
 interface BioSource
          The BioSource is the original source material before any treatment events.
 interface Compound
          A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).
 interface LabeledExtract
          LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties).
 interface Treatment
          The process by which a biomaterial is created (from source biomaterials).
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioMaterial.impl
 

Classes in gov.nih.nci.mageom.domain.BioMaterial.impl that implement Identifiable
 class BioMaterialImpl
          BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
 class BioSampleImpl
          BioSamples are products of treatments that are of interest.
 class BioSourceImpl
          The BioSource is the original source material before any treatment events.
 class CompoundImpl
          A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).
 class LabeledExtractImpl
          LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties).
 class TreatmentImpl
          The process by which a biomaterial is created (from source biomaterials).
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioSequence
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioSequence
 interface BioSequence
          A BioSequence is a representation of a DNA, RNA, or protein sequence.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.BioSequence.impl
 

Classes in gov.nih.nci.mageom.domain.BioSequence.impl that implement Identifiable
 class BioSequenceImpl
          A BioSequence is a representation of a DNA, RNA, or protein sequence.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Description
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Description
 interface Database
          An address to a repository.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Description.impl
 

Classes in gov.nih.nci.mageom.domain.Description.impl that implement Identifiable
 class DatabaseImpl
          An address to a repository.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.DesignElement
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.DesignElement
 interface CompositeCompositeMap
          A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
 interface CompositeSequence
          A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
 interface DesignElement
          An element of an array.
 interface Feature
          An intended position on an array.
 interface FeatureReporterMap
          A FeatureReporterMap is the description of how source features are transformed into a target reporter.
 interface Reporter
          A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
 interface ReporterCompositeMap
          A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.DesignElement.impl
 

Classes in gov.nih.nci.mageom.domain.DesignElement.impl that implement Identifiable
 class CompositeCompositeMapImpl
          A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
 class CompositeSequenceImpl
          A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
 class DesignElementImpl
          An element of an array.
 class FeatureImpl
          An intended position on an array.
 class FeatureReporterMapImpl
          A FeatureReporterMap is the description of how source features are transformed into a target reporter.
 class ReporterCompositeMapImpl
          A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.
 class ReporterImpl
          A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Experiment
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Experiment
 interface Experiment
          The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
 interface ExperimentalFactor
          ExperimentFactors are the dependent variables of an experiment (e.g.
 interface FactorValue
          The value for a ExperimentalFactor
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Experiment.impl
 

Classes in gov.nih.nci.mageom.domain.Experiment.impl that implement Identifiable
 class ExperimentalFactorImpl
          ExperimentFactors are the dependent variables of an experiment (e.g.
 class ExperimentImpl
          The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
 class FactorValueImpl
          The value for a ExperimentalFactor
 

Uses of Identifiable in gov.nih.nci.mageom.domain.HigherLevelAnalysis
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.HigherLevelAnalysis
 interface BioAssayDataCluster
          A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl
 

Classes in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl that implement Identifiable
 class BioAssayDataClusterImpl
          A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.impl
 

Classes in gov.nih.nci.mageom.domain.impl that implement Identifiable
 class IdentifiableImpl
          An Identifiable class is one that has an unambiguous reference within the scope.
 

Methods in gov.nih.nci.mageom.domain.impl that return Identifiable
 Identifiable[] IdentifiableImpl.searchIdentifiables(IdentifiableSearchCriteria criteria)
          Returns an array of Identifiable objects that satisfy the given IdentifiableSearchCriteria.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Protocol
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Protocol
 interface Hardware
          Hardware represents the hardware used.
 interface Parameter
          A Parameter is a replaceable value in a Parameterizable class.
 interface Parameterizable
          The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
 interface Protocol
          A Protocol is a parameterizable description of a method.
 interface Software
          Software represents the software used.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.Protocol.impl
 

Classes in gov.nih.nci.mageom.domain.Protocol.impl that implement Identifiable
 class HardwareImpl
          Hardware represents the hardware used.
 class ParameterImpl
          A Parameter is a replaceable value in a Parameterizable class.
 class ParameterizableImpl
          The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
 class ProtocolImpl
          A Protocol is a parameterizable description of a method.
 class SoftwareImpl
          Software represents the software used.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.QuantitationType
 

Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.QuantitationType
 interface ConfidenceIndicator
          Indication of some measure of confidence for a standard quantitation type.
 interface DerivedSignal
          A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements.
 interface Error
          Error measurement of a quantitation.
 interface ExpectedValue
          Indication of what value is expected of the associated standard quantitation type.
 interface Failed
          Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay.
 interface MeasuredSignal
          Best measure from feature extraction as to the presence and intensity of the signal.
 interface PresentAbsent
          Indicates relative presence or absence.
 interface PValue
          Measurement of the accuracy of a quantitation.
 interface QuantitationType
          A method for calculating a single datum of the matrix (e.g.
 interface Ratio
          The ratio of two or more signals, typically between two channels.
 interface SpecializedQuantitationType
          User defined quantitation type.
 interface StandardQuantitationType
          Superclass for the named quantitation type.
 

Uses of Identifiable in gov.nih.nci.mageom.domain.QuantitationType.impl
 

Classes in gov.nih.nci.mageom.domain.QuantitationType.impl that implement Identifiable
 class ConfidenceIndicatorImpl
          Indication of some measure of confidence for a standard quantitation type.
 class DerivedSignalImpl
          A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements.
 class ErrorImpl
          Error measurement of a quantitation.
 class ExpectedValueImpl
          Indication of what value is expected of the associated standard quantitation type.
 class FailedImpl
          Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay.
 class MeasuredSignalImpl
          Best measure from feature extraction as to the presence and intensity of the signal.
 class PresentAbsentImpl
          Indicates relative presence or absence.
 class PValueImpl
          Measurement of the accuracy of a quantitation.
 class QuantitationTypeImpl
          A method for calculating a single datum of the matrix (e.g.
 class RatioImpl
          The ratio of two or more signals, typically between two channels.
 class SpecializedQuantitationTypeImpl
          User defined quantitation type.
 class StandardQuantitationTypeImpl
          Superclass for the named quantitation type.