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

Packages that use MAGEOMObject
gov.nih.nci.common.persistence.enhanced   
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.BQS.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.impl   
gov.nih.nci.mageom.domain.Measurement.impl   
gov.nih.nci.mageom.domain.Protocol.impl   
gov.nih.nci.mageom.domain.QuantitationType.impl   
 

Uses of MAGEOMObject in gov.nih.nci.common.persistence.enhanced
 

Method parameters in gov.nih.nci.common.persistence.enhanced with type arguments of type MAGEOMObject
protected  java.lang.Long[] BaseQueryImpl.getIds(java.util.Collection<MAGEOMObject> mageOMObjects)
           
protected  java.util.Collection<java.lang.Long> BaseQueryImpl.getIdsAsCollection(java.util.Collection<MAGEOMObject> mageOMObjects)
           
 

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

Subclasses of MAGEOMObject 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 ArrayManufactureDeviationImpl
          Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g.
 class ArrayManufactureImpl
          Describes the process by which arrays are produced.
 class FeatureDefectImpl
          Stores the defect information for a feature.
 class FiducialImpl
          A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid.
 class ManufactureLIMSBiomaterialImpl
          Stores the location from which a biomaterial was obtained.
 class ManufactureLIMSImpl
          Information on the physical production of arrays within the laboratory.
 class PositionDeltaImpl
          The delta the feature was actually printed on the array from the position specified for the feature in the array design.
 class ZoneDefectImpl
          Stores the defect information for a zone.
 

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

Subclasses of MAGEOMObject 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 ZoneGroupImpl
          Specifies a repeating area on an array.
 class ZoneImpl
          Specifies the location of a zone on an array.
 class ZoneLayoutImpl
          Specifies the layout of features in a rectangular grid.
 

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

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.AuditAndSecurity.impl
 class AuditImpl
          Tracks information on the contact that creates or modifies an object.
 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 MAGEOMObject in gov.nih.nci.mageom.domain.BioAssay.impl
 

Subclasses of MAGEOMObject 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 MAGEOMObject in gov.nih.nci.mageom.domain.BioAssayData.impl
 

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BioAssayData.impl
 class BioAssayDataImpl
          Represents the dataset created when the BioAssays are created.
 class BioAssayDatumImpl
          A single cell of the quantitation, bioAssay, designElement matrix.
 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 BioAssayMappingImpl
          Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.
 class BioDataCubeImpl
          A three-dimensional cube representation of the data.
 class BioDataTuplesImpl
          A relational, tuple representation of the data.
 class BioDataValuesImpl
          The actual values for the BioAssayCube.
 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 DesignElementMappingImpl
          Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension.
 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 QuantitationTypeMappingImpl
          Container of the mappings of the input QuantitationType dimensions to the output QuantitationType dimension.
 class ReporterDimensionImpl
          Specialized DesignElementDimension to hold Reporters.
 class TransformationImpl
          The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays.
 

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

Subclasses of MAGEOMObject 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 MAGEOMObject in gov.nih.nci.mageom.domain.BioMaterial.impl
 

Subclasses of MAGEOMObject 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 BioMaterialMeasurementImpl
          A BioMaterialMeasurement is a pairing of a source BioMaterial and an amount (Measurement) of that BioMaterial.
 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 CompoundMeasurementImpl
          A CompoundMeasurement is a pairing of a source Compound and an amount (Measurement) of that Compound.
 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 MAGEOMObject in gov.nih.nci.mageom.domain.BioSequence.impl
 

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BioSequence.impl
 class BioSequenceImpl
          A BioSequence is a representation of a DNA, RNA, or protein sequence.
 class SeqFeatureImpl
          Represents, in general, what would be a GenBank Feature Table annotation for a sequence.
 class SeqFeatureLocationImpl
          The location of the SeqFeature annotation.
 class SequencePositionImpl
          Designates the position of the Feature in its BioSequence.
 

Uses of MAGEOMObject in gov.nih.nci.mageom.domain.BQS.impl
 

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BQS.impl
 class BibliographicReferenceImpl
          Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference.
 

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

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Description.impl
 class DatabaseEntryImpl
          A reference to a record in a database.
 class DatabaseImpl
          An address to a repository.
 class DescriptionImpl
          A free text description of an object.
 class ExternalReferenceImpl
          A reference to the originating source for the object.
 class OntologyEntryImpl
          A single entry from an ontology or a controlled vocabulary.
 

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

Subclasses of MAGEOMObject 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 CompositePositionImpl
          The location in the compositeSequence target's sequence to which a source compositeSequence maps.
 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 FeatureInformationImpl
          As part of the map information, allows the association of one or more differences in the BioMaterial on a feature from the BioMaterial of the Reporter.
 class FeatureLocationImpl
          Specifies where a feature is located relative to a grid.
 class FeatureReporterMapImpl
          A FeatureReporterMap is the description of how source features are transformed into a target reporter.
 class MismatchInformationImpl
          Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.
 class PositionImpl
          Specifies a position on an array.
 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.
 class ReporterPositionImpl
          The location in the composite target's sequence to which a source reporter maps.
 

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

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Experiment.impl
 class ExperimentalFactorImpl
          ExperimentFactors are the dependent variables of an experiment (e.g.
 class ExperimentDesignImpl
          The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.
 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 MAGEOMObject in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl
 

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl
 class BioAssayDataClusterImpl
          A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.
 class NodeContentsImpl
          The contents of a node for any or all of the three Dimensions.
 class NodeImpl
          An individual component of a clustering.
 class NodeValueImpl
          A value associated with the Node that can rank it in relation to the other nodes produced by the clustering algorithm.
 

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

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.impl
 class DescribableImpl
          Abstract class that allows subclasses to inherit the association to Description, for detailed annotations such as Ontology entries and Database references, the association to Audit, for tracking changes, and the association to Security for indicating permissions.
 class ExtendableImpl
          Abstract class that specifies for subclasses an association to NameValueTypes.
 class IdentifiableImpl
          An Identifiable class is one that has an unambiguous reference within the scope.
 class NameValueTypeImpl
          A tuple designed to store data, keyed by a name and type.
 

Uses of MAGEOMObject in gov.nih.nci.mageom.domain.Measurement.impl
 

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Measurement.impl
 class ConcentrationUnitImpl
          Concentration
 class DistanceUnitImpl
          Distance
 class MassUnitImpl
          Mass
 class MeasurementImpl
          A Measurement is a quantity with a unit.
 class QuantityUnitImpl
          Quantity
 class TemperatureUnitImpl
          Temperature
 class TimeUnitImpl
          Time
 class UnitImpl
          The unit is a strict enumeration of types.
 class VolumeUnitImpl
          Volume
 

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

Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Protocol.impl
 class HardwareApplicationImpl
          The use of a piece of hardware with the requisite Parameters and ParameterValues.
 class HardwareImpl
          Hardware represents the hardware used.
 class ParameterImpl
          A Parameter is a replaceable value in a Parameterizable class.
 class ParameterizableApplicationImpl
          The interface that is the use of a Parameterizable class.
 class ParameterizableImpl
          The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
 class ParameterValueImpl
          The value of a Parameter.
 class ProtocolApplicationImpl
          The use of a protocol with the requisite Parameters and ParameterValues.
 class ProtocolImpl
          A Protocol is a parameterizable description of a method.
 class SoftwareApplicationImpl
          The use of a piece of software with the requisite Parameters and ParameterValues.
 class SoftwareImpl
          Software represents the software used.
 

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

Subclasses of MAGEOMObject 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.