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| Uses of MAGEOMObject in gov.nih.nci.common.persistence.enhanced |
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| Method parameters in gov.nih.nci.common.persistence.enhanced with type arguments of type MAGEOMObject | |
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protected java.lang.Long[] |
BaseQueryImpl.getIds(java.util.Collection<MAGEOMObject> mageOMObjects)
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protected java.util.Collection<java.lang.Long> |
BaseQueryImpl.getIdsAsCollection(java.util.Collection<MAGEOMObject> mageOMObjects)
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| Uses of MAGEOMObject in gov.nih.nci.mageom.domain.Array.impl |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Array.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.ArrayDesign.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.AuditAndSecurity.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BioAssay.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BioAssayData.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BioEvent.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BioMaterial.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BioSequence.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.BQS.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Description.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.DesignElement.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Experiment.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Measurement.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.Protocol.impl | |
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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 |
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| Subclasses of MAGEOMObject in gov.nih.nci.mageom.domain.QuantitationType.impl | |
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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. |
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