A B C D E F G H I J K L M N O P Q R S T U V W Y Z

D

D - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV

DATA - Static variable in class org.biomage.tools.generate_er.CreateMageER

table type is data

database - Variable in class org.biomage.Description.DatabaseEntry

Reference to the database where the DataEntry instance can be found.

Database - class org.biomage.Description.Database.

An address to a repository.

database_list - Variable in class org.biomage.Description.Description_package

An address to a repository.

Database() - Constructor for class org.biomage.Description.Database

Default constructor.

Database(Attributes) - Constructor for class org.biomage.Description.Database

Attribute constructor.

DatabaseEntry - class org.biomage.Description.DatabaseEntry.

A reference to a record in a database.

DatabaseEntry() - Constructor for class org.biomage.Description.DatabaseEntry

Default constructor.

DatabaseEntry(Attributes) - Constructor for class org.biomage.Description.DatabaseEntry

Attribute constructor.

databaseReferences - Variable in class org.biomage.Description.Description

References to entries in databases.

DataColumn - class org.biomage.tools.generate_er.DataColumn.

DataColumn() - Constructor for class org.biomage.tools.generate_er.DataColumn

Description: Constructor for the DataColumn object.

dataType - Variable in class org.biomage.HigherLevelAnalysis.NodeValue

The data type of the any element.

dataType - Variable in class org.biomage.Protocol.Parameter

The type of data generated by the parameter i.e.

dataType - Variable in class org.biomage.QuantitationType.QuantitationType

The specific type for the quantitations.

DBQ - Variable in class org.biomage.BioAssayData.BioDataCube.Order

defectType - Variable in class org.biomage.Array.ZoneDefect

Indicates the type of defect (e.g.

defectType - Variable in class org.biomage.Array.FeatureDefect

Indicates the type of defect (e.g.

DEGREE_C - Variable in class org.biomage.Measurement.TemperatureUnit.UnitNameCV

DEGREE_F - Variable in class org.biomage.Measurement.TemperatureUnit.UnitNameCV

DerivedBioAssay - class org.biomage.BioAssay.DerivedBioAssay.

A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.

DerivedBioAssay() - Constructor for class org.biomage.BioAssay.DerivedBioAssay

Default constructor.

DerivedBioAssay(Attributes) - Constructor for class org.biomage.BioAssay.DerivedBioAssay

Attribute constructor.

derivedBioAssayData - Variable in class org.biomage.BioAssay.DerivedBioAssay

The data associated with the DerivedBioAssay.

DerivedBioAssayData - class org.biomage.BioAssayData.DerivedBioAssayData.

The output of a transformation event.

DerivedBioAssayData() - Constructor for class org.biomage.BioAssayData.DerivedBioAssayData

Default constructor.

DerivedBioAssayData(Attributes) - Constructor for class org.biomage.BioAssayData.DerivedBioAssayData

Attribute constructor.

derivedBioAssayDataTarget - Variable in class org.biomage.BioAssayData.Transformation

The association between the DerivedBioAssayData and the Transformation event that produced it.

DerivedSignal - class org.biomage.QuantitationType.DerivedSignal.

A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements.

DerivedSignal() - Constructor for class org.biomage.QuantitationType.DerivedSignal

Default constructor.

DerivedSignal(Attributes) - Constructor for class org.biomage.QuantitationType.DerivedSignal

Attribute constructor.

Describable - class org.biomage.Common.Describable.

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.

Describable() - Constructor for class org.biomage.Common.Describable

Default constructor.

Describable(Attributes) - Constructor for class org.biomage.Common.Describable

Attribute constructor.

Description - class org.biomage.Description.Description.

A free text description of an object.

description_package - Variable in class org.biomage.Common.MAGEJava

The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.

Description_package - class org.biomage.Description.Description_package.

The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.

Description_package.Database_list - class org.biomage.Description.Description_package.Database_list.

Inner list class for holding multiple entries for attribute database.

Description_package.Database_list() - Constructor for class org.biomage.Description.Description_package.Database_list

Description_package() - Constructor for class org.biomage.Description.Description_package

Default constructor.

Description_package(Attributes) - Constructor for class org.biomage.Description.Description_package

Attribute constructor.

Description() - Constructor for class org.biomage.Description.Description

Default constructor.

Description(Attributes) - Constructor for class org.biomage.Description.Description

Attribute constructor.

descriptions - Variable in class org.biomage.Common.Describable

Free hand text descriptions.

designElement - Variable in class org.biomage.BioAssayData.BioAssayDatum

The DesignElement associated with the value of the BioAssayDatum.

DesignElement - class org.biomage.DesignElement.DesignElement.

An element of an array.

designElement_package - Variable in class org.biomage.Common.MAGEJava

The classes of this package are the contained classes of the ArrayDesign and describe through the DesignElements what is intended to be at each location of the Array.

DesignElement_package - class org.biomage.DesignElement.DesignElement_package.

The classes of this package are the contained classes of the ArrayDesign and describe through the DesignElements what is intended to be at each location of the Array.

DesignElement_package.CompositeCompositeMap_list - class org.biomage.DesignElement.DesignElement_package.CompositeCompositeMap_list.

Inner list class for holding multiple entries for attribute compositeCompositeMap.

DesignElement_package.CompositeCompositeMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.CompositeCompositeMap_list

DesignElement_package.CompositeSequence_list - class org.biomage.DesignElement.DesignElement_package.CompositeSequence_list.

Inner list class for holding multiple entries for attribute compositeSequence.

DesignElement_package.CompositeSequence_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.CompositeSequence_list

DesignElement_package.FeatureReporterMap_list - class org.biomage.DesignElement.DesignElement_package.FeatureReporterMap_list.

Inner list class for holding multiple entries for attribute featureReporterMap.

DesignElement_package.FeatureReporterMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.FeatureReporterMap_list

DesignElement_package.Reporter_list - class org.biomage.DesignElement.DesignElement_package.Reporter_list.

Inner list class for holding multiple entries for attribute reporter.

DesignElement_package.Reporter_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.Reporter_list

DesignElement_package.ReporterCompositeMap_list - class org.biomage.DesignElement.DesignElement_package.ReporterCompositeMap_list.

Inner list class for holding multiple entries for attribute reporterCompositeMap.

DesignElement_package.ReporterCompositeMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.ReporterCompositeMap_list

DesignElement_package() - Constructor for class org.biomage.DesignElement.DesignElement_package

Default constructor.

DesignElement_package(Attributes) - Constructor for class org.biomage.DesignElement.DesignElement_package

Attribute constructor.

DesignElement() - Constructor for class org.biomage.DesignElement.DesignElement

Default constructor.

DesignElement(Attributes) - Constructor for class org.biomage.DesignElement.DesignElement

Attribute constructor.

designElementDimension - Variable in class org.biomage.BioAssayData.BioAssayData

The DesignElements of the BioAssayData.

designElementDimension - Variable in class org.biomage.HigherLevelAnalysis.NodeContents

The relevant DesignElements for this NodeContents from the BioAssayData.

DesignElementDimension - class org.biomage.BioAssayData.DesignElementDimension.

An ordered list of designElements.

designElementDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package

An ordered list of designElements.

DesignElementDimension() - Constructor for class org.biomage.BioAssayData.DesignElementDimension

Default constructor.

DesignElementDimension(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementDimension

Attribute constructor.

DesignElementGroup - class org.biomage.ArrayDesign.DesignElementGroup.

The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.

DesignElementGroup() - Constructor for class org.biomage.ArrayDesign.DesignElementGroup

Default constructor.

DesignElementGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.DesignElementGroup

Attribute constructor.

DesignElementMap - class org.biomage.BioAssayData.DesignElementMap.

A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.

DesignElementMap() - Constructor for class org.biomage.BioAssayData.DesignElementMap

Default constructor.

DesignElementMap(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementMap

Attribute constructor.

designElementMapping - Variable in class org.biomage.BioAssayData.Transformation

The collection of mappings for the DesignElements.

DesignElementMapping - class org.biomage.BioAssayData.DesignElementMapping.

Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension.

DesignElementMapping() - Constructor for class org.biomage.BioAssayData.DesignElementMapping

Default constructor.

DesignElementMapping(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementMapping

Attribute constructor.

designElementMaps - Variable in class org.biomage.BioAssayData.DesignElementMapping

The maps for the DesignElements.

designProviders - Variable in class org.biomage.ArrayDesign.ArrayDesign

The primary contact for information on the array design

DISTANCE - Variable in class org.biomage.Measurement.Measurement.KindCV

distanceUnit - Variable in class org.biomage.Array.PositionDelta

The unit for the attributes.

distanceUnit - Variable in class org.biomage.Array.Fiducial

The units the fiducial is measured in.

distanceUnit - Variable in class org.biomage.Array.ArrayGroup

The unit of the measurement attributes.

distanceUnit - Variable in class org.biomage.ArrayDesign.ZoneLayout

Unit of the ZoneLayout attributes.

distanceUnit - Variable in class org.biomage.ArrayDesign.ZoneGroup

Unit for the ZoneGroup attributes.

distanceUnit - Variable in class org.biomage.ArrayDesign.Zone

Unit for the Zone attributes.

distanceUnit - Variable in class org.biomage.ArrayDesign.FeatureGroup

The unit for the feature measures.

distanceUnit - Variable in class org.biomage.DesignElement.Position

The units of the x, y positions.

DistanceUnit - class org.biomage.Measurement.DistanceUnit.

Distance

DistanceUnit.UnitNameCV - class org.biomage.Measurement.DistanceUnit.UnitNameCV.

Inner class for the enumeration values that the attribute unitNameCV can assume.

DistanceUnit() - Constructor for class org.biomage.Measurement.DistanceUnit

Default constructor.

DistanceUnit(Attributes) - Constructor for class org.biomage.Measurement.DistanceUnit

Attribute constructor.

DL - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV

DQB - Variable in class org.biomage.BioAssayData.BioDataCube.Order