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Uses of Identifiable in gov.nih.nci.caarray.services.mageloader |
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Methods in gov.nih.nci.caarray.services.mageloader that return Identifiable | |
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Identifiable |
MAGEMLImportManagerDB.getByIdentifier(java.lang.Class identifiableClass,
java.lang.String identifier,
boolean insertIfNotFound)
Get object by identifier, if not there it makes it when insertIfNotFound is true. |
Identifiable |
MAGEMLImportManagerDB.resolveIdentifiable(org.xml.sax.Attributes attrs,
Identifiable parsedIdentifiable)
Get object by identifier, if not there it makes it. |
Methods in gov.nih.nci.caarray.services.mageloader with parameters of type Identifiable | |
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Identifiable |
MAGEMLImportManagerDB.resolveIdentifiable(org.xml.sax.Attributes attrs,
Identifiable parsedIdentifiable)
Get object by identifier, if not there it makes it. |
void |
DatabaseImportMAGEReader.saveMAGEMLCallBack(Identifiable importedObject)
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Uses of Identifiable in gov.nih.nci.caarray.services.util.db |
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Methods in gov.nih.nci.caarray.services.util.db that return Identifiable | |
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Identifiable |
ManagerDB.getIdentifiable(java.lang.Class identifiableClass,
java.lang.String identifier)
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Uses of Identifiable in gov.nih.nci.caarray.services.util.mage |
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Constructors in gov.nih.nci.caarray.services.util.mage with parameters of type Identifiable | |
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MAGEWriter(Identifiable topMostObjectForGeneration)
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Uses of Identifiable in gov.nih.nci.caarray.services.util.ojb |
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Methods in gov.nih.nci.caarray.services.util.ojb with parameters of type Identifiable | |
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static void |
PBLifeCycleListenerMAGEIdentifierAssigner.assignIdentifier(Identifiable obj)
Assign the Identifier value to an MAGE object using the format |
Uses of Identifiable in org.biomage.Array |
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Subclasses of Identifiable in org.biomage.Array | |
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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. |
Uses of Identifiable in org.biomage.ArrayDesign |
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Subclasses of Identifiable in org.biomage.ArrayDesign | |
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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. |
Uses of Identifiable in org.biomage.AuditAndSecurity |
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Subclasses of Identifiable in org.biomage.AuditAndSecurity | |
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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 Identifiable in org.biomage.BioAssay |
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Subclasses of Identifiable in org.biomage.BioAssay | |
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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 Identifiable in org.biomage.BioAssayData |
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Subclasses of Identifiable in org.biomage.BioAssayData | |
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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 |
CompositeSequenceDimension
Specialized DesignElementDimension to hold CompositeSequences. |
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 |
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 |
ReporterDimension
Specialized DesignElementDimension to hold Reporters. |
class |
Transformation
The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. |
Uses of Identifiable in org.biomage.BioEvent |
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Subclasses of Identifiable in org.biomage.BioEvent | |
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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 Identifiable in org.biomage.BioMaterial |
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Subclasses of Identifiable in org.biomage.BioMaterial | |
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class |
BioMaterial
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... |
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 |
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 Identifiable in org.biomage.BioSequence |
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Subclasses of Identifiable in org.biomage.BioSequence | |
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class |
BioSequence
A BioSequence is a representation of a DNA, RNA, or protein sequence. |
Uses of Identifiable in org.biomage.Description |
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Subclasses of Identifiable in org.biomage.Description | |
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class |
Database
An address to a repository. |
Uses of Identifiable in org.biomage.DesignElement |
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Subclasses of Identifiable in org.biomage.DesignElement | |
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class |
CompositeCompositeMap
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. |
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 |
FeatureReporterMap
A FeatureReporterMap is the description of how source features are transformed into a target reporter. |
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. |
Uses of Identifiable in org.biomage.Experiment |
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Subclasses of Identifiable in org.biomage.Experiment | |
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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 |
FactorValue
The value for a ExperimentalFactor |
Uses of Identifiable in org.biomage.HigherLevelAnalysis |
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Subclasses of Identifiable in org.biomage.HigherLevelAnalysis | |
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class |
BioAssayDataCluster
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes. |
Uses of Identifiable in org.biomage.Protocol |
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Subclasses of Identifiable in org.biomage.Protocol | |
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class |
Hardware
Hardware represents the hardware used. |
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 |
Protocol
A Protocol is a parameterizable description of a method. |
class |
Software
Software represents the software used. |
Uses of Identifiable in org.biomage.QuantitationType |
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Subclasses of Identifiable in org.biomage.QuantitationType | |
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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. |
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