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Uses of SecuredElementItf in gov.nih.nci.caarray.common.delegate |
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Methods in gov.nih.nci.caarray.common.delegate that return SecuredElementItf | |
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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 | |
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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 |
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Methods in gov.nih.nci.caarray.services.security that return SecuredElementItf | |
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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 | |
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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 |
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Methods in gov.nih.nci.caarray.services.security.ejb that return SecuredElementItf | |
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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 | |
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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 |
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Methods in gov.nih.nci.caarray.services.security.test that return SecuredElementItf | |
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SecuredElementItf |
SecuredElementBuilder.build(java.util.Properties props)
|
SecuredElementItf |
MAGEMLImportSecuredElementBuilder.build(java.util.Properties props)
|
Uses of SecuredElementItf in gov.nih.nci.caarray.services.util |
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Classes in gov.nih.nci.caarray.services.util that implement SecuredElementItf | |
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class |
BaseSecuredElement
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Methods in gov.nih.nci.caarray.services.util that return SecuredElementItf | |
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static SecuredElementItf[] |
SecurityUtils.searchOwner(SecuredElementItf[] results)
|
static SecuredElementItf[] |
SecurityUtils.searchOwnerOnly(SecuredElementItf[] results)
|
static SecuredElementItf[] |
SecurityUtils.searchVisibility(ProtectionGroupData visibility,
SecuredElementItf[] results,
java.lang.String[] requiredRoles)
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Methods in gov.nih.nci.caarray.services.util with parameters of type SecuredElementItf | |
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static ProtectionGroupData[] |
EJBUtils.getProtectionGroupsFromObject(SecuredElementItf itf)
|
static SecuredElementItf[] |
SecurityUtils.searchOwner(SecuredElementItf[] results)
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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 |
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Classes in org.biomage.Array that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.ArrayDesign that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.AuditAndSecurity that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.BioAssay that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.BioAssayData that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.BioEvent that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.BioMaterial that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.BioSequence that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.BQS that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.Common that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.Description that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.Description.Ontology that implement SecuredElementItf | |
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class |
Age
|
class |
BioMaterialCharacteristic
|
class |
Biometrics
|
class |
ChromosomalAberration
|
Uses of SecuredElementItf in org.biomage.DesignElement |
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Classes in org.biomage.DesignElement that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.Experiment that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.HigherLevelAnalysis that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.Measurement that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.Protocol that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.QuantitationType that implement SecuredElementItf | |
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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 |
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Classes in org.biomage.tools.helpers that implement SecuredElementItf | |
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class |
MGEDOntologyClassEntry
|
class |
MGEDOntologyEntry
|
static class |
MGEDOntologyEntry.OntologyDatabaseEntry
|
class |
MGEDOntologyPropertyEntry
|
|
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