Uses of Class
gov.nih.nci.mageom.domain.impl.IdentifiableImpl

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

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

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.Array.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.ArrayDesign.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.ArrayDesign.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.AuditAndSecurity.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.AuditAndSecurity.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.BioAssay.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.BioAssay.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.BioAssayData.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.BioAssayData.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.BioEvent.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.BioEvent.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.BioMaterial.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.BioMaterial.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.BioSequence.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.BioSequence.impl
 class BioSequenceImpl
          A BioSequence is a representation of a DNA, RNA, or protein sequence.
 

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

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.Description.impl
 class DatabaseImpl
          An address to a repository.
 

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

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.DesignElement.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.Experiment.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.Experiment.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl
 

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

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

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.Protocol.impl
 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 IdentifiableImpl in gov.nih.nci.mageom.domain.QuantitationType.impl
 

Subclasses of IdentifiableImpl in gov.nih.nci.mageom.domain.QuantitationType.impl
 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.