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

P

Parameter - class org.biomage.Protocol.Parameter.

A Parameter is a replaceable value in a Parameterizable class.

Parameter() - Constructor for class org.biomage.Protocol.Parameter

Default constructor.

Parameter(Attributes) - Constructor for class org.biomage.Protocol.Parameter

Attribute constructor.

Parameterizable - class org.biomage.Protocol.Parameterizable.

The Parameterizable interface encapsulates the association of Parameters with ParameterValues.

Parameterizable() - Constructor for class org.biomage.Protocol.Parameterizable

Default constructor.

Parameterizable(Attributes) - Constructor for class org.biomage.Protocol.Parameterizable

Attribute constructor.

ParameterizableApplication - class org.biomage.Protocol.ParameterizableApplication.

The interface that is the use of a Parameterizable class.

ParameterizableApplication() - Constructor for class org.biomage.Protocol.ParameterizableApplication

Default constructor.

ParameterizableApplication(Attributes) - Constructor for class org.biomage.Protocol.ParameterizableApplication

Attribute constructor.

parameters - Variable in class org.biomage.BQS.BibliographicReference

Criteria that can be used to look up the reference in a repository.

parameterType - Variable in class org.biomage.Protocol.ParameterValue

The parameter this value is for.

parameterTypes - Variable in class org.biomage.Protocol.Parameterizable

The description of the parameters for the Parameterizable class instance.

ParameterValue - class org.biomage.Protocol.ParameterValue.

The value of a Parameter.

ParameterValue() - Constructor for class org.biomage.Protocol.ParameterValue

Default constructor.

ParameterValue(Attributes) - Constructor for class org.biomage.Protocol.ParameterValue

Attribute constructor.

parameterValues - Variable in class org.biomage.Protocol.ParameterizableApplication

The parameter values for this Parameterizable Application.

parent - Variable in class org.biomage.AuditAndSecurity.Organization

The containing organization (the university or business which a lab belongs to, etc.)

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

performer - Variable in class org.biomage.AuditAndSecurity.Audit

The contact for creating or changing the instance referred to by the Audit.

performers - Variable in class org.biomage.Protocol.ProtocolApplication

The people who performed the protocol.

Person - class org.biomage.AuditAndSecurity.Person.

A person for which the attributes are self describing.

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

Default constructor.

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

Attribute constructor.

PG - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV

PhysicalArrayDesign - class org.biomage.ArrayDesign.PhysicalArrayDesign.

A design that is expected to be used to manufacture physical arrays.

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

Default constructor.

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

Attribute constructor.

physicalBioAssay - Variable in class org.biomage.BioAssay.BioAssayTreatment

The set of treatments undergone by this PhysicalBioAssay.

PhysicalBioAssay - class org.biomage.BioAssay.PhysicalBioAssay.

A bioAssay created by the bioAssayCreation event (e.g.

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

Default constructor.

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

Attribute constructor.

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

The Images associated with this PhysicalBioAssay by ImageAcquisition.

physicalBioAssaySource - Variable in class org.biomage.BioAssay.FeatureExtraction

The PhysicalBioAssay used in the FeatureExtraction event.

physicalBioAssayTarget - Variable in class org.biomage.BioAssay.BioAssayCreation

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

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

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

PM - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV

PMOL - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV

polymerType - Variable in class org.biomage.BioSequence.BioSequence

A choice of protein, RNA, or DNA.

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

The position, relative to the upper left corner, of the fiducial

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

The position of the feature on the array, relative to the top, left corner.

Position - class org.biomage.DesignElement.Position.

Specifies a position on an array.

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

Default constructor.

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

Attribute constructor.

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

How the zone deviates in position from the ArrayDesign.

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

How the feature deviates in position from the ArrayDesign.

PositionDelta - class org.biomage.Array.PositionDelta.

The delta the feature was actually printed on the array from the position specified for the feature in the array design.

PositionDelta() - Constructor for class org.biomage.Array.PositionDelta

Default constructor.

PositionDelta(Attributes) - Constructor for class org.biomage.Array.PositionDelta

Attribute constructor.

PresentAbsent - class org.biomage.QuantitationType.PresentAbsent.

Indicates relative presence or absence.

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

Default constructor.

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

Attribute constructor.

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

full name of the primary key for tables

PrimaryKey - class org.biomage.tools.generate_er.PrimaryKey.

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

Description: Constructor for the PrimaryKey object.

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

Description: Constructor for the PrimaryKey object.

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

producerTransformation - Variable in class org.biomage.BioAssayData.DerivedBioAssayData

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

propertySets - Variable in class org.biomage.Common.NameValueType

Allows nested specification of name/value pairs

propertySets - Variable in class org.biomage.Common.Extendable

Allows specification of name/value pairs.

protocol - Variable in class org.biomage.Protocol.ProtocolApplication

The protocol that is being used.

Protocol - class org.biomage.Protocol.Protocol.

A Protocol is a parameterizable description of a method.

protocol_list - Variable in class org.biomage.Protocol.Protocol_package

A Protocol is a parameterizable description of a method.

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

Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol.

Protocol_package - class org.biomage.Protocol.Protocol_package.

Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol.

Protocol_package.Hardware_list - class org.biomage.Protocol.Protocol_package.Hardware_list.

Inner list class for holding multiple entries for attribute hardware.

Protocol_package.Hardware_list() - Constructor for class org.biomage.Protocol.Protocol_package.Hardware_list

Protocol_package.Protocol_list - class org.biomage.Protocol.Protocol_package.Protocol_list.

Inner list class for holding multiple entries for attribute protocol.

Protocol_package.Protocol_list() - Constructor for class org.biomage.Protocol.Protocol_package.Protocol_list

Protocol_package.Software_list - class org.biomage.Protocol.Protocol_package.Software_list.

Inner list class for holding multiple entries for attribute software.

Protocol_package.Software_list() - Constructor for class org.biomage.Protocol.Protocol_package.Software_list

Protocol_package() - Constructor for class org.biomage.Protocol.Protocol_package

Default constructor.

Protocol_package(Attributes) - Constructor for class org.biomage.Protocol.Protocol_package

Attribute constructor.

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

Default constructor.

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

Attribute constructor.

ProtocolApplication - class org.biomage.Protocol.ProtocolApplication.

The use of a protocol with the requisite Parameters and ParameterValues.

ProtocolApplication() - Constructor for class org.biomage.Protocol.ProtocolApplication

Default constructor.

ProtocolApplication(Attributes) - Constructor for class org.biomage.Protocol.ProtocolApplication

Attribute constructor.

protocolApplications - Variable in class org.biomage.Array.ArrayManufacture

The protocols followed in the manufacturing of the arrays.

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

Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.

protocolApplications - Variable in class org.biomage.BioEvent.BioEvent

The applied protocols to the BioEvent.

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

The providers of the Experiment, its data and annotation.

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

{@inheritDoc} Note that this method will always return null.

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

{@inheritDoc} Note that this method will always return null.

PValue - class org.biomage.QuantitationType.PValue.

Measurement of the accuracy of a quantitation.

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

Default constructor.

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

Attribute constructor.