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

C

category - Variable in class org.biomage.Experiment.ExperimentalFactor

The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).

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

CHANGE - Variable in class org.biomage.Measurement.Measurement.Type

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

The optional channel associated with the QuantitationType.

Channel - class org.biomage.BioAssay.Channel.

A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.

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

A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.

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

Default constructor.

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

Attribute constructor.

channels - Variable in class org.biomage.BioAssay.Image

The channels captured in this image.

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

Channels can be non-null for all subclasses.

characteristics - Variable in class org.biomage.BioMaterial.BioMaterial

Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.

characters(char[], int, int) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

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

Description: check to see if there is the case that A has two one_to_many relationships with B and get the same name

childIdentifier - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef

childType - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef

classConstructorMap - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler

clusterBioAssayData - Variable in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster

The BioAssayData whose values were used by the cluster algorithm.

CM - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV

componentCompounds - Variable in class org.biomage.BioMaterial.Compound

The Compounds and their amounts used to create this Compound.

composite - Variable in class org.biomage.DesignElement.CompositePosition

A source CompositeSequence that is part of a target CompositeSequence

CompositeCompositeMap - class org.biomage.DesignElement.CompositeCompositeMap.

A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.

compositeCompositeMap_list - Variable in class org.biomage.DesignElement.DesignElement_package

A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.

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

Default constructor.

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

Attribute constructor.

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

A map to the compositeSequences that compose this CompositeSequence.

CompositeGroup - class org.biomage.ArrayDesign.CompositeGroup.

Allows specification of the type of Composite Design Element.

compositeGroup_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package

Allows specification of the type of Composite Design Element.

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

Default constructor.

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

Attribute constructor.

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

The grouping of like CompositeSequence together.

CompositePosition - class org.biomage.DesignElement.CompositePosition.

The location in the compositeSequence target's sequence to which a source compositeSequence maps.

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

Default constructor.

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

Attribute constructor.

compositePositionSources - Variable in class org.biomage.DesignElement.CompositeCompositeMap

Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur.

compositeSequence - Variable in class org.biomage.DesignElement.ReporterCompositeMap

A map to the reporters that compose this CompositeSequence.

compositeSequence - Variable in class org.biomage.DesignElement.CompositeCompositeMap

A map to the compositeSequences that compose this CompositeSequence.

CompositeSequence - class org.biomage.DesignElement.CompositeSequence.

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.

compositeSequence_list - Variable in class org.biomage.DesignElement.DesignElement_package

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.

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

Default constructor.

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

Attribute constructor.

CompositeSequenceDimension - class org.biomage.BioAssayData.CompositeSequenceDimension.

Specialized DesignElementDimension to hold CompositeSequences.

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

Default constructor.

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

Attribute constructor.

compositeSequences - Variable in class org.biomage.ArrayDesign.CompositeGroup

The compositeSequences that belong to this group.

compositeSequences - Variable in class org.biomage.BioAssayData.CompositeSequenceDimension

The CompositeSequences for this Dimension.

compound - Variable in class org.biomage.BioMaterial.CompoundMeasurement

A Compound to be used to create another Compound.

Compound - class org.biomage.BioMaterial.Compound.

A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).

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

A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).

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

Default constructor.

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

Attribute constructor.

CompoundMeasurement - class org.biomage.BioMaterial.CompoundMeasurement.

A CompoundMeasurement is a pairing of a source Compound and an amount (Measurement) of that Compound.

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

Default constructor.

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

Attribute constructor.

compoundMeasurements - Variable in class org.biomage.BioMaterial.Treatment

The compounds and their amounts used in the treatment.

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

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

ConcentrationUnit - class org.biomage.Measurement.ConcentrationUnit.

Concentration

ConcentrationUnit.UnitNameCV - class org.biomage.Measurement.ConcentrationUnit.UnitNameCV.

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

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

Default constructor.

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

Attribute constructor.

ConfidenceIndicator - class org.biomage.QuantitationType.ConfidenceIndicator.

Indication of some measure of confidence for a standard quantitation type.

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

Default constructor.

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

Attribute constructor.

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

The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.

Contact - class org.biomage.AuditAndSecurity.Contact.

A contact is either a person or an organization.

contact_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

A contact is either a person or an organization.

Contact() - Constructor for class org.biomage.AuditAndSecurity.Contact

Default constructor.

Contact(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Contact

Attribute constructor.

contacts - Variable in class org.biomage.Description.Database

Information on the contacts for the database

containedFeatures - Variable in class org.biomage.BioAssayData.FeatureDimension

The features for this dimension.

containsValue(Object) - Method in class org.biomage.tools.xmlutils.MultiHashtable

{@inheritDoc}

containsValue(Object) - Method in class org.biomage.tools.xmlutils.MultiHashMap

{@inheritDoc}

controlFeatures - Variable in class org.biomage.DesignElement.Feature

Associates features with their control features.

controlledFeatures - Variable in class org.biomage.DesignElement.Feature

Associates features with their control features.

controlType - Variable in class org.biomage.DesignElement.DesignElement

If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)

coordinate - Variable in class org.biomage.BioSequence.SeqFeatureLocation

At which base pairs or amino acid this SeqFeature begins and ends.

cppBodyIndent - Static variable in class org.biomage.tools.helpers.StringOutputHelpers

createAssociationStack() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Factory method to instantiate the Associations Stack.

createClassConstructorMap() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Factory method to instantiate the Class->Constructor Map.

createIdentifierMap() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Factory method to instantiate the String->Object (identifiers->identified objects) Map.

createIndex(AssociationColumn, String, String) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: create a Index object for a foreign key fk_oto does not have index fk_mto has index fk_mtm has index

createLinkColumn(String) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: create a column for a linking table

createLinkingKey(AssociationColumn, AssociationColumn) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: create a linkingKey object and set into the table

createLinkingTable(CreateFile, String) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: create a linking table

CreateMageER - class org.biomage.tools.generate_er.CreateMageER.

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

Description: Constructor for the CreateMageER object.

createMAGEJava() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Factory method to instantiate the MAGEJava object.

createMAGEObject(String, Attributes) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

createMethodsMap() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Factory method to instantiate the String->Method MultiMap.

createObjectStack() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Factory method to instantiate the created Objects Stack.

createPackageDir(String, String) - Static method in class org.biomage.tools.helpers.StringOutputHelpers

Description: Creates the directory for the package.

createUnique(Vector) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: create a Unique object which takes a vector of columns

createUnresolvedRefStack() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

Factory method to instantiate the UnresolvedRefs Stack.

createValuesSet() - Method in class org.biomage.tools.xmlutils.MultiHashtable

Factory method for instantiating objects of type Set for use as the containers of multiple values mapped to a single key.

createValuesSet() - Method in class org.biomage.tools.xmlutils.MultiHashMap

Factory method for instantiating objects of type Set for use as the containers of multiple values mapped to a single key.

CREATION - Variable in class org.biomage.AuditAndSecurity.Audit.Action