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

B

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

BibliographicReference - class org.biomage.BQS.BibliographicReference.

Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference.

BibliographicReference() - Constructor for class org.biomage.BQS.BibliographicReference

Default constructor.

BibliographicReference(Attributes) - Constructor for class org.biomage.BQS.BibliographicReference

Attribute constructor.

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

References to existing literature.

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

The BioAssay associated with the value of the BioAssayDatum.

BioAssay - class org.biomage.BioAssay.BioAssay.

An abstract class which represents both physical and computational groupings of arrays and biomaterials.

bioAssay_list - Variable in class org.biomage.BioAssay.BioAssay_package

An abstract class which represents both physical and computational groupings of arrays and biomaterials.

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

Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images.

BioAssay_package - class org.biomage.BioAssay.BioAssay_package.

Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images.

BioAssay_package.BioAssay_list - class org.biomage.BioAssay.BioAssay_package.BioAssay_list.

Inner list class for holding multiple entries for attribute bioAssay.

BioAssay_package.BioAssay_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.BioAssay_list

BioAssay_package.Channel_list - class org.biomage.BioAssay.BioAssay_package.Channel_list.

Inner list class for holding multiple entries for attribute channel.

BioAssay_package.Channel_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.Channel_list

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

Default constructor.

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

Attribute constructor.

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

Default constructor.

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

Attribute constructor.

bioAssayCreation - Variable in class org.biomage.BioAssay.PhysicalBioAssay

The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.

BioAssayCreation - class org.biomage.BioAssay.BioAssayCreation.

The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.

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

Default constructor.

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

Attribute constructor.

bioAssayData - Variable in class org.biomage.Experiment.Experiment

The collection of BioAssayDatas for this Experiment.

BioAssayData - class org.biomage.BioAssayData.BioAssayData.

Represents the dataset created when the BioAssays are created.

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

Represents the dataset created when the BioAssays are created.

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

The classes defined here provide data and the information and annotation on the derivation of that data.

BioAssayData_package - class org.biomage.BioAssayData.BioAssayData_package.

The classes defined here provide data and the information and annotation on the derivation of that data.

BioAssayData_package.BioAssayData_list - class org.biomage.BioAssayData.BioAssayData_package.BioAssayData_list.

Inner list class for holding multiple entries for attribute bioAssayData.

BioAssayData_package.BioAssayData_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayData_list

BioAssayData_package.BioAssayDimension_list - class org.biomage.BioAssayData.BioAssayData_package.BioAssayDimension_list.

Inner list class for holding multiple entries for attribute bioAssayDimension.

BioAssayData_package.BioAssayDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayDimension_list

BioAssayData_package.BioAssayMap_list - class org.biomage.BioAssayData.BioAssayData_package.BioAssayMap_list.

Inner list class for holding multiple entries for attribute bioAssayMap.

BioAssayData_package.BioAssayMap_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayMap_list

BioAssayData_package.DesignElementDimension_list - class org.biomage.BioAssayData.BioAssayData_package.DesignElementDimension_list.

Inner list class for holding multiple entries for attribute designElementDimension.

BioAssayData_package.DesignElementDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.DesignElementDimension_list

BioAssayData_package.QuantitationTypeDimension_list - class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeDimension_list.

Inner list class for holding multiple entries for attribute quantitationTypeDimension.

BioAssayData_package.QuantitationTypeDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeDimension_list

BioAssayData_package.QuantitationTypeMap_list - class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeMap_list.

Inner list class for holding multiple entries for attribute quantitationTypeMap.

BioAssayData_package.QuantitationTypeMap_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeMap_list

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

Default constructor.

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

Attribute constructor.

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

Default constructor.

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

Attribute constructor.

BioAssayDataCluster - class org.biomage.HigherLevelAnalysis.BioAssayDataCluster.

A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.

bioAssayDataCluster_list - Variable in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package

A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.

BioAssayDataCluster() - Constructor for class org.biomage.HigherLevelAnalysis.BioAssayDataCluster

Default constructor.

BioAssayDataCluster(Attributes) - Constructor for class org.biomage.HigherLevelAnalysis.BioAssayDataCluster

Attribute constructor.

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

The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.

BioAssayDatum - class org.biomage.BioAssayData.BioAssayDatum.

A single cell of the quantitation, bioAssay, designElement matrix.

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

Default constructor.

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

Attribute constructor.

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

The BioAssays of the BioAssayData.

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

The relevant BioAssays for this NodeContents from the BioAssayData.

BioAssayDimension - class org.biomage.BioAssayData.BioAssayDimension.

An ordered list of bioAssays.

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

An ordered list of bioAssays.

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

Default constructor.

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

Attribute constructor.

bioAssayFactorValues - Variable in class org.biomage.BioAssay.BioAssay

The values that this BioAssay is associated with for the experiment.

BioAssayMap - class org.biomage.BioAssayData.BioAssayMap.

The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.

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

The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.

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

Default constructor.

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

Attribute constructor.

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

The collection of mappings for the BioAssays.

BioAssayMapping - class org.biomage.BioAssayData.BioAssayMapping.

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

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

Default constructor.

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

Attribute constructor.

bioAssayMaps - Variable in class org.biomage.BioAssayData.BioAssayMapping

The maps for the BioAssays.

bioAssayMapTarget - Variable in class org.biomage.BioAssayData.BioAssayMap

The DerivedBioAssay that is produced by the sources of the BioAssayMap.

bioAssays - Variable in class org.biomage.BioAssayData.BioAssayDimension

The BioAssays for this Dimension

bioAssays - Variable in class org.biomage.Experiment.Experiment

The collection of BioAssays for this Experiment.

BioAssayTreatment - class org.biomage.BioAssay.BioAssayTreatment.

The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).

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

Default constructor.

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

Attribute constructor.

bioAssayTreatments - Variable in class org.biomage.BioAssay.PhysicalBioAssay

The set of treatments undergone by this PhysicalBioAssay.

bioAssayTupleData - Variable in class org.biomage.BioAssayData.BioDataTuples

The collection of BioAssayData tuples.

BioDataCube - class org.biomage.BioAssayData.BioDataCube.

A three-dimensional cube representation of the data.

BioDataCube.Order - class org.biomage.BioAssayData.BioDataCube.Order.

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

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

Default constructor.

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

Attribute constructor.

BioDataTuples - class org.biomage.BioAssayData.BioDataTuples.

A relational, tuple representation of the data.

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

Default constructor.

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

Attribute constructor.

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

The data values of the BioAssayData.

BioDataValues - class org.biomage.BioAssayData.BioDataValues.

The actual values for the BioAssayCube.

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

Default constructor.

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

Attribute constructor.

BioEvent - class org.biomage.BioEvent.BioEvent.

An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).

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

An abstract class representing an event that takes sources of some type to produce a target of some type.

BioEvent_package - class org.biomage.BioEvent.BioEvent_package.

An abstract class representing an event that takes sources of some type to produce a target of some type.

BioEvent_package() - Constructor for class org.biomage.BioEvent.BioEvent_package

Default constructor.

BioEvent_package(Attributes) - Constructor for class org.biomage.BioEvent.BioEvent_package

Attribute constructor.

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

Default constructor.

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

Attribute constructor.

biologicalCharacteristics - Variable in class org.biomage.DesignElement.CompositeSequence

The annotation on the BioSequence this CompositeSequence represents.

bioMaterial - Variable in class org.biomage.Array.ManufactureLIMS

The BioMaterial used for the feature.

bioMaterial - Variable in class org.biomage.BioMaterial.BioMaterialMeasurement

A source BioMaterial for a treatment.

BioMaterial - class org.biomage.BioMaterial.BioMaterial.

BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...

bioMaterial_list - Variable in class org.biomage.BioMaterial.BioMaterial_package

BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...

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

The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay.

BioMaterial_package - class org.biomage.BioMaterial.BioMaterial_package.

The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay.

BioMaterial_package.BioMaterial_list - class org.biomage.BioMaterial.BioMaterial_package.BioMaterial_list.

Inner list class for holding multiple entries for attribute bioMaterial.

BioMaterial_package.BioMaterial_list() - Constructor for class org.biomage.BioMaterial.BioMaterial_package.BioMaterial_list

BioMaterial_package.Compound_list - class org.biomage.BioMaterial.BioMaterial_package.Compound_list.

Inner list class for holding multiple entries for attribute compound.

BioMaterial_package.Compound_list() - Constructor for class org.biomage.BioMaterial.BioMaterial_package.Compound_list

BioMaterial_package() - Constructor for class org.biomage.BioMaterial.BioMaterial_package

Default constructor.

BioMaterial_package(Attributes) - Constructor for class org.biomage.BioMaterial.BioMaterial_package

Attribute constructor.

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

Default constructor.

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

Attribute constructor.

BioMaterialMeasurement - class org.biomage.BioMaterial.BioMaterialMeasurement.

A BioMaterialMeasurement is a pairing of a source BioMaterial and an amount (Measurement) of that BioMaterial.

BioMaterialMeasurement() - Constructor for class org.biomage.BioMaterial.BioMaterialMeasurement

Default constructor.

BioMaterialMeasurement(Attributes) - Constructor for class org.biomage.BioMaterial.BioMaterialMeasurement

Attribute constructor.

BioSample - class org.biomage.BioMaterial.BioSample.

BioSamples are products of treatments that are of interest.

BioSample() - Constructor for class org.biomage.BioMaterial.BioSample

Default constructor.

BioSample(Attributes) - Constructor for class org.biomage.BioMaterial.BioSample

Attribute constructor.

BioSequence - class org.biomage.BioSequence.BioSequence.

A BioSequence is a representation of a DNA, RNA, or protein sequence.

bioSequence_list - Variable in class org.biomage.BioSequence.BioSequence_package

A BioSequence is a representation of a DNA, RNA, or protein sequence.

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

Describes a known gene or sequence.

BioSequence_package - class org.biomage.BioSequence.BioSequence_package.

Describes a known gene or sequence.

BioSequence_package.BioSequence_list - class org.biomage.BioSequence.BioSequence_package.BioSequence_list.

Inner list class for holding multiple entries for attribute bioSequence.

BioSequence_package.BioSequence_list() - Constructor for class org.biomage.BioSequence.BioSequence_package.BioSequence_list

BioSequence_package() - Constructor for class org.biomage.BioSequence.BioSequence_package

Default constructor.

BioSequence_package(Attributes) - Constructor for class org.biomage.BioSequence.BioSequence_package

Attribute constructor.

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

Default constructor.

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

Attribute constructor.

BioSource - class org.biomage.BioMaterial.BioSource.

The BioSource is the original source material before any treatment events.

BioSource() - Constructor for class org.biomage.BioMaterial.BioSource

Default constructor.

BioSource(Attributes) - Constructor for class org.biomage.BioMaterial.BioSource

Attribute constructor.

BOTH - Variable in class org.biomage.BioSequence.SeqFeature.Basis

BOTTOM - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition

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

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

Allows a reference to an article, book or other publication to be specified for searching repositories.

BQS_package - class org.biomage.BQS.BQS_package.

Allows a reference to an article, book or other publication to be specified for searching repositories.

BQS_package() - Constructor for class org.biomage.BQS.BQS_package

Default constructor.

BQS_package(Attributes) - Constructor for class org.biomage.BQS.BQS_package

Attribute constructor.

buildTables(String, Vector) - Method in class org.biomage.tools.generate_er.CreateMageER