Uses of Interface
gov.nih.nci.caarray.services.security.intf.SecuredElementItf

Packages that use SecuredElementItf
gov.nih.nci.caarray.common.delegate   
gov.nih.nci.caarray.services.security   
gov.nih.nci.caarray.services.security.ejb   
gov.nih.nci.caarray.services.security.test   
gov.nih.nci.caarray.services.util   
org.biomage.Array   
org.biomage.ArrayDesign   
org.biomage.AuditAndSecurity   
org.biomage.BioAssay   
org.biomage.BioAssayData   
org.biomage.BioEvent   
org.biomage.BioMaterial   
org.biomage.BioSequence   
org.biomage.BQS   
org.biomage.Common   
org.biomage.Description   
org.biomage.Description.Ontology   
org.biomage.DesignElement   
org.biomage.Experiment   
org.biomage.HigherLevelAnalysis   
org.biomage.Measurement   
org.biomage.Protocol   
org.biomage.QuantitationType   
org.biomage.tools.helpers   
 

Uses of SecuredElementItf in gov.nih.nci.caarray.common.delegate
 

Methods in gov.nih.nci.caarray.common.delegate that return SecuredElementItf
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf SecurityManagerDelegate.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf CaSecurityManagerDelegate.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Deprecated.  
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Deprecated.  
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessOwnerElement(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessOwnerElement(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessOwnerElementOnly(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessOwnerElementOnly(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 

Methods in gov.nih.nci.caarray.common.delegate with parameters of type SecuredElementItf
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessElement(SecuredElementItf[] objects, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf SecurityManagerDelegate.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf CaSecurityManagerDelegate.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Deprecated.  
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Deprecated.  
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessOwnerElement(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessOwnerElement(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerDelegate.canUserAccessOwnerElementOnly(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerDelegate.canUserAccessOwnerElementOnly(SecuredElementItf[] objects)
          Checks if the user can access the securedElement for this Object.
 

Uses of SecuredElementItf in gov.nih.nci.caarray.services.security
 

Methods in gov.nih.nci.caarray.services.security that return SecuredElementItf
 SecuredElementItf SecurityServiceObj.authorizeUser(java.lang.String loginName, java.lang.String[] roles, java.lang.String applicationName, SecuredElementItf object)
          Overloaded to support isEditable.
 SecuredElementItf[] SecurityServiceObj.authorizeUser(java.lang.String loginName, java.lang.String[] roles, java.lang.String applicationName, SecuredElementItf[] objects)
          Returns the given users with role's access permission to a collection of protection element.
 SecuredElementItf[] SecurityServiceObj.authorizeUser(java.lang.String loginName, java.lang.String[] roles, java.lang.String applicationName, SecuredElementItf[] objects, ProtectionGroupData[] protectionGroups)
          Returns the given users with role's access permission to a collection of protection element.
 SecuredElementItf[] SecurityServiceObj.authorizeUserOwner(java.lang.String loginName, java.lang.String applicationName, SecuredElementItf[] objects)
          Returns the given users with role's access permission to a collection of protection element.
 SecuredElementItf[] SecurityServiceObj.authorizeUserOwnerOnly(java.lang.String loginName, java.lang.String applicationName, SecuredElementItf[] objects)
          Returns the given users with role's access permission to a collection of protection element.
protected  SecuredElementItf[] SecurityServiceObj.getPermittedObjects(java.util.LinkedHashMap objectEntries)
           
 

Methods in gov.nih.nci.caarray.services.security with parameters of type SecuredElementItf
 SecuredElementItf SecurityServiceObj.authorizeUser(java.lang.String loginName, java.lang.String[] roles, java.lang.String applicationName, SecuredElementItf object)
          Overloaded to support isEditable.
 SecuredElementItf[] SecurityServiceObj.authorizeUser(java.lang.String loginName, java.lang.String[] roles, java.lang.String applicationName, SecuredElementItf[] objects)
          Returns the given users with role's access permission to a collection of protection element.
 SecuredElementItf[] SecurityServiceObj.authorizeUser(java.lang.String loginName, java.lang.String[] roles, java.lang.String applicationName, SecuredElementItf[] objects, ProtectionGroupData[] protectionGroups)
          Returns the given users with role's access permission to a collection of protection element.
 SecuredElementItf[] SecurityServiceObj.authorizeUserOwner(java.lang.String loginName, java.lang.String applicationName, SecuredElementItf[] objects)
          Returns the given users with role's access permission to a collection of protection element.
 SecuredElementItf[] SecurityServiceObj.authorizeUserOwnerOnly(java.lang.String loginName, java.lang.String applicationName, SecuredElementItf[] objects)
          Returns the given users with role's access permission to a collection of protection element.
 

Uses of SecuredElementItf in gov.nih.nci.caarray.services.security.ejb
 

Methods in gov.nih.nci.caarray.services.security.ejb that return SecuredElementItf
 SecuredElementItf[] SecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf SecurityManagerEJB.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf CaSecurityManagerEJB.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessOwnerElement(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessOwnerElement(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessOwnerElementOnly(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessOwnerElementOnly(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 

Methods in gov.nih.nci.caarray.services.security.ejb with parameters of type SecuredElementItf
 SecuredElementItf[] SecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessElement(SecuredElementItf[] objectIds, java.lang.String[] roleIds, ProtectionGroupData[] protectionGroups)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf SecurityManagerEJB.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf CaSecurityManagerEJB.canUserAccessElement(SecuredElementItf object, java.lang.String[] roleIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessElement(java.lang.String userId, SecuredElementItf[] objectIds, java.lang.String[] roleIds)
          Checks if the user can access the securedElemet for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessOwnerElement(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessOwnerElement(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] SecurityManagerEJB.canUserAccessOwnerElementOnly(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 SecuredElementItf[] CaSecurityManagerEJB.canUserAccessOwnerElementOnly(SecuredElementItf[] objectIds)
          Checks if the user can access the securedElement for this Object.
 

Uses of SecuredElementItf in gov.nih.nci.caarray.services.security.test
 

Methods in gov.nih.nci.caarray.services.security.test that return SecuredElementItf
 SecuredElementItf SecuredElementBuilder.build(java.util.Properties props)
           
 SecuredElementItf MAGEMLImportSecuredElementBuilder.build(java.util.Properties props)
           
 

Uses of SecuredElementItf in gov.nih.nci.caarray.services.util
 

Classes in gov.nih.nci.caarray.services.util that implement SecuredElementItf
 class BaseSecuredElement
           
 

Methods in gov.nih.nci.caarray.services.util that return SecuredElementItf
static SecuredElementItf[] SecurityUtils.searchOwner(SecuredElementItf[] results)
           
static SecuredElementItf[] SecurityUtils.searchOwnerOnly(SecuredElementItf[] results)
           
static SecuredElementItf[] SecurityUtils.searchVisibility(ProtectionGroupData visibility, SecuredElementItf[] results, java.lang.String[] requiredRoles)
           
 

Methods in gov.nih.nci.caarray.services.util with parameters of type SecuredElementItf
static ProtectionGroupData[] EJBUtils.getProtectionGroupsFromObject(SecuredElementItf itf)
           
static SecuredElementItf[] SecurityUtils.searchOwner(SecuredElementItf[] results)
           
static SecuredElementItf[] SecurityUtils.searchOwnerOnly(SecuredElementItf[] results)
           
static SecuredElementItf[] SecurityUtils.searchVisibility(ProtectionGroupData visibility, SecuredElementItf[] results, java.lang.String[] requiredRoles)
           
 

Uses of SecuredElementItf in org.biomage.Array
 

Classes in org.biomage.Array that implement SecuredElementItf
 class Array
          The physical substrate along with its features and their annotation
 class ArrayGroup
          An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
 class ArrayManufacture
          Describes the process by which arrays are produced.
 class ArrayManufactureDeviation
          Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g.
 class FeatureDefect
          Stores the defect information for a feature.
 class Fiducial
          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 ManufactureLIMS
          Information on the physical production of arrays within the laboratory.
 class ManufactureLIMSBiomaterial
          Stores the location from which a biomaterial was obtained.
 class PositionDelta
          The delta the feature was actually printed on the array from the position specified for the feature in the array design.
 class ZoneDefect
          Stores the defect information for a zone.
 

Uses of SecuredElementItf in org.biomage.ArrayDesign
 

Classes in org.biomage.ArrayDesign that implement SecuredElementItf
 class ArrayDesign
          Describes the design of an gene expression layout.
 class CompositeGroup
          Allows specification of the type of Composite Design Element.
 class DesignElementGroup
          The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
 class FeatureGroup
          A collection of like features.
 class PhysicalArrayDesign
          A design that is expected to be used to manufacture physical arrays.
 class ReporterGroup
          Allows specification of the type of Reporter Design Element.
 class Zone
          Specifies the location of a zone on an array.
 class ZoneGroup
          Specifies a repeating area on an array.
 class ZoneLayout
          Specifies the layout of features in a rectangular grid.
 

Uses of SecuredElementItf in org.biomage.AuditAndSecurity
 

Classes in org.biomage.AuditAndSecurity that implement SecuredElementItf
 class Audit
          Tracks information on the contact that creates or modifies an object.
 class Contact
          A contact is either a person or an organization.
 class Organization
          Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
 class Person
          A person for which the attributes are self describing.
 class Security
          Permission information for an object as to ownership, write and read permissions.
 class SecurityGroup
          Groups contacts together based on their security privileges.
 class User
          A user for which the attributes are self describing.
 

Uses of SecuredElementItf in org.biomage.BioAssay
 

Classes in org.biomage.BioAssay that implement SecuredElementItf
 class BioAssay
          An abstract class which represents both physical and computational groupings of arrays and biomaterials.
 class BioAssayCreation
          The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.
 class BioAssayTreatment
          The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).
 class Channel
          A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
 class DerivedBioAssay
          A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
 class FeatureExtraction
          The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay.
 class Hybridization
          The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array.
 class Image
          An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay).
 class ImageAcquisition
          The process by which an image is generated (typically scanning).
 class MeasuredBioAssay
          A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
 class PhysicalBioAssay
          A bioAssay created by the bioAssayCreation event (e.g.
 

Uses of SecuredElementItf in org.biomage.BioAssayData
 

Classes in org.biomage.BioAssayData that implement SecuredElementItf
 class BioAssayData
          Represents the dataset created when the BioAssays are created.
 class BioAssayDimension
          An ordered list of bioAssays.
 class BioAssayMap
          The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
 class BioAssayMapping
          Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.
 class BioAssayTuple
          Transformed container to specify a BioAssay and the Design Elements and their data for that BioAssay.
 class BioDataCube
          A three-dimensional cube representation of the data.
 class BioDataTuples
          A relational, tuple representation of the data.
 class BioDataValues
          The actual values for the BioAssayCube.
 class CompositeSequenceDimension
          Specialized DesignElementDimension to hold CompositeSequences.
 class DataExternal
          Transformed class to associate external data to the BioAssayDataCube
 class DataInternal
          Transformed class to associate whitespaced delimited data to the BioAssayDataCube
 class Datum
          Transformed container to hold a value.
 class DerivedBioAssayData
          The output of a transformation event.
 class DesignElementDimension
          An ordered list of designElements.
 class DesignElementMap
          A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
 class DesignElementMapping
          Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension.
 class DesignElementTuple
          Transformed container to specify a DesignElement and QuantitationTypes for that Element.
 class FeatureDimension
          Specialized DesignElementDimension to hold Features.
 class MeasuredBioAssayData
          The data associated with the MeasuredBioAssay produced by FeatureExtraction.
 class QuantitationTypeDimension
          An ordered list of quantitationTypes.
 class QuantitationTypeMap
          A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
 class QuantitationTypeMapping
          Container of the mappings of the input QuantitationType dimensions to the output QuantitationType dimension.
 class QuantitationTypeTuple
          Transformed container to specify a Quantitation Type and the value for that Type.
 class ReporterDimension
          Specialized DesignElementDimension to hold Reporters.
 class Transformation
          The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays.
 

Uses of SecuredElementItf in org.biomage.BioEvent
 

Classes in org.biomage.BioEvent that implement SecuredElementItf
 class BioEvent
          An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
 class Map
          A Map is the description of how sources are transformed into a target.
 

Uses of SecuredElementItf in org.biomage.BioMaterial
 

Classes in org.biomage.BioMaterial that implement SecuredElementItf
 class BioMaterial
          BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
 class BioMaterialMeasurement
          A BioMaterialMeasurement is a pairing of a source BioMaterial and an amount (Measurement) of that BioMaterial.
 class BioSample
          BioSamples are products of treatments that are of interest.
 class BioSource
          The BioSource is the original source material before any treatment events.
 class Compound
          A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).
 class CompoundMeasurement
          A CompoundMeasurement is a pairing of a source Compound and an amount (Measurement) of that Compound.
 class LabeledExtract
          LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties).
 class Treatment
          The process by which a biomaterial is created (from source biomaterials).
 

Uses of SecuredElementItf in org.biomage.BioSequence
 

Classes in org.biomage.BioSequence that implement SecuredElementItf
 class BioSequence
          A BioSequence is a representation of a DNA, RNA, or protein sequence.
 class SeqFeature
          Represents, in general, what would be a GenBank Feature Table annotation for a sequence.
 class SeqFeatureLocation
          The location of the SeqFeature annotation.
 class SequencePosition
          Designates the position of the Feature in its BioSequence.
 

Uses of SecuredElementItf in org.biomage.BQS
 

Classes in org.biomage.BQS that implement SecuredElementItf
 class BibliographicReference
          Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference.
 

Uses of SecuredElementItf in org.biomage.Common
 

Classes in org.biomage.Common that implement SecuredElementItf
 class 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.
 class Extendable
          Abstract class that specifies for subclasses an association to NameValueTypes.
 class Identifiable
          An Identifiable class is one that has an unambiguous reference within the scope.
 

Uses of SecuredElementItf in org.biomage.Description
 

Classes in org.biomage.Description that implement SecuredElementItf
 class Database
          An address to a repository.
 class DatabaseEntry
          A reference to a record in a database.
 class Description
          A free text description of an object.
 class ExternalReference
          A reference to the originating source for the object.
 class OntologyEntry
          A single entry from an ontology or a controlled vocabulary.
 

Uses of SecuredElementItf in org.biomage.Description.Ontology
 

Classes in org.biomage.Description.Ontology that implement SecuredElementItf
 class Age
           
 class BioMaterialCharacteristic
           
 class Biometrics
           
 class ChromosomalAberration
           
 

Uses of SecuredElementItf in org.biomage.DesignElement
 

Classes in org.biomage.DesignElement that implement SecuredElementItf
 class CompositeCompositeMap
          A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
 class CompositePosition
          The location in the compositeSequence target's sequence to which a source compositeSequence maps.
 class CompositeSequence
          A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
 class DesignElement
          An element of an array.
 class Feature
          An intended position on an array.
 class FeatureInformation
          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 FeatureLocation
          Specifies where a feature is located relative to a grid.
 class FeatureReporterMap
          A FeatureReporterMap is the description of how source features are transformed into a target reporter.
 class MismatchInformation
          Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.
 class Position
          Specifies a position on an array.
 class Reporter
          A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
 class ReporterCompositeMap
          A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.
 class ReporterPosition
          The location in the composite target's sequence to which a source reporter maps.
 

Uses of SecuredElementItf in org.biomage.Experiment
 

Classes in org.biomage.Experiment that implement SecuredElementItf
 class Experiment
          The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
 class ExperimentalFactor
          ExperimentFactors are the dependent variables of an experiment (e.g.
 class ExperimentDesign
          The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.
 class FactorValue
          The value for a ExperimentalFactor
 

Uses of SecuredElementItf in org.biomage.HigherLevelAnalysis
 

Classes in org.biomage.HigherLevelAnalysis that implement SecuredElementItf
 class BioAssayDataCluster
          A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.
 class Node
          An individual component of a clustering.
 class NodeContents
          The contents of a node for any or all of the three Dimensions.
 class NodeValue
          A value associated with the Node that can rank it in relation to the other nodes produced by the clustering algorithm.
 

Uses of SecuredElementItf in org.biomage.Measurement
 

Classes in org.biomage.Measurement that implement SecuredElementItf
 class ConcentrationUnit
          Concentration
 class DistanceUnit
          Distance
 class MassUnit
          Mass
 class Measurement
          A Measurement is a quantity with a unit.
 class OtherUnit
           
 class QuantityUnit
          Quantity
 class TemperatureUnit
          Temperature
 class TimeUnit
          Time
 class Unit
          The unit is a strict enumeration of types.
 class VolumeUnit
          Volume
 

Uses of SecuredElementItf in org.biomage.Protocol
 

Classes in org.biomage.Protocol that implement SecuredElementItf
 class Hardware
          Hardware represents the hardware used.
 class HardwareApplication
          The use of a piece of hardware with the requisite Parameters and ParameterValues.
 class Parameter
          A Parameter is a replaceable value in a Parameterizable class.
 class Parameterizable
          The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
 class ParameterizableApplication
          The interface that is the use of a Parameterizable class.
 class ParameterValue
          The value of a Parameter.
 class Protocol
          A Protocol is a parameterizable description of a method.
 class ProtocolApplication
          The use of a protocol with the requisite Parameters and ParameterValues.
 class Software
          Software represents the software used.
 class SoftwareApplication
          The use of a piece of software with the requisite Parameters and ParameterValues.
 

Uses of SecuredElementItf in org.biomage.QuantitationType
 

Classes in org.biomage.QuantitationType that implement SecuredElementItf
 class ConfidenceIndicator
          Indication of some measure of confidence for a standard quantitation type.
 class DerivedSignal
          A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements.
 class Error
          Error measurement of a quantitation.
 class ExpectedValue
          Indication of what value is expected of the associated standard quantitation type.
 class Failed
          Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay.
 class MeasuredSignal
          Best measure from feature extraction as to the presence and intensity of the signal.
 class PresentAbsent
          Indicates relative presence or absence.
 class PValue
          Measurement of the accuracy of a quantitation.
 class QuantitationType
          A method for calculating a single datum of the matrix (e.g.
 class Ratio
          The ratio of two or more signals, typically between two channels.
 class SpecializedQuantitationType
          User defined quantitation type.
 class StandardQuantitationType
          Superclass for the named quantitation type.
 

Uses of SecuredElementItf in org.biomage.tools.helpers
 

Classes in org.biomage.tools.helpers that implement SecuredElementItf
 class MGEDOntologyClassEntry
           
 class MGEDOntologyEntry
           
static class MGEDOntologyEntry.OntologyDatabaseEntry
           
 class MGEDOntologyPropertyEntry