Uses of Interface
com.genologics.ri.Linkable

Packages that use Linkable

Package	Description
com.genologics.ri	The root package of the classes generated (originally) from the Clarity schemas.
com.genologics.ri.artifact
com.genologics.ri.artifactgroup
com.genologics.ri.automation
com.genologics.ri.configuration
com.genologics.ri.container
com.genologics.ri.containertype
com.genologics.ri.controltype
com.genologics.ri.file
com.genologics.ri.instrument
com.genologics.ri.instrumenttype
com.genologics.ri.lab
com.genologics.ri.permission
com.genologics.ri.process
com.genologics.ri.processexecution
com.genologics.ri.processtemplate
com.genologics.ri.processtype
com.genologics.ri.project
com.genologics.ri.protocolconfiguration
com.genologics.ri.queue
com.genologics.ri.reagentkit
com.genologics.ri.reagentlot
com.genologics.ri.reagenttype
com.genologics.ri.researcher
com.genologics.ri.role
com.genologics.ri.routing
com.genologics.ri.sample
com.genologics.ri.stage
com.genologics.ri.step
com.genologics.ri.stepconfiguration
com.genologics.ri.workflowconfiguration
org.cruk.clarity.api	The main public package of the Clarity API.
org.cruk.clarity.api.impl	Concrete implementation classes of the Clarity API.

Uses of Linkable in com.genologics.ri

Subinterfaces of Linkable in com.genologics.ri

Modifier and Type	Interface	Description
interface	LimsEntity<E extends LimsEntity<E>>	Interface for all objects that are real LIMS entities (i.e. not links or other references).
interface	LimsEntityLink<E extends LimsEntity<E>>	Interface for links to LimsEntity objects.
interface	LimsEntityLinkable<E extends LimsEntity<E>>	Interface for entities and links to entities that are identifiable in the system (i.e. have a LIMS id).
interface	LimsLink<E extends Locatable>	Interface for classes that are links to real LIMS objects.

Classes in com.genologics.ri that implement Linkable

Modifier and Type	Class	Description
class	ContainerLink	Container is a child element of location and provides a URI linking to the detailed representation of the Container for the location.
class	Location	Location provides a URI linking to the detailed representation of a Container along with the well location within that Container.

Methods in com.genologics.ri with parameters of type Linkable

Modifier and Type	Method	Description
Link	Links.add(Linkable<?> link)

Constructors in com.genologics.ri with parameters of type Linkable

Modifier	Constructor	Description
	ContainerLink(Linkable<Container> link)
	Link(Linkable<?> limsLink)
	Location(Linkable<Container> container, String position)

Uses of Linkable in com.genologics.ri.artifact

Classes in com.genologics.ri.artifact that implement Linkable

Modifier and Type	Class	Description
class	Artifact	The detailed representation of an Artifact.
class	ArtifactGroupLink	Artifact group is a child element of Artifact and provides a URI linking to the detailed representation of the artifact group that the Artifact belongs to.
class	ArtifactLink	Artifact-link is a child element type of artifacts and provides a URI linking to the detailed representation of an artifact.
class	ControlTypeLink	Provide a URI linking to the control type if this artifact is a control sample.
class	DemuxArtifactSample	The details of a sample that is part of a pooled artifact.
class	DemuxLink	Identifies the resource that will demultiplex this artifact.
class	DemuxSourceArtifact
class	ParentProcessLink	Parent-process is a child element of Artifact and provides a URI linking to the detailed representation of the process that produced the Artifact.
class	PoolStep	The details of the pooling step that created the pooled sample(s).
class	SampleLink	Sample is a child element of Artifact and provides a URI linking to the detailed representation of a submitted Sample for the Artifact.
class	WorkflowStage	Provides links to workflow stages, stage names and their respective statuses.

Methods in com.genologics.ri.artifact with parameters of type Linkable

Modifier and Type	Method	Description
ArtifactGroupLink	Artifact.addArtifactGroup(Linkable<ArtifactGroup> link)
void	DemuxLink.setArtifact(Linkable<DemuxArtifact> artifact)
void	DemuxSourceArtifact.setArtifact(Linkable<Artifact> artifact)
void	Artifact.setControlType(Linkable<ControlType> link)
void	Artifact.setDemux(Linkable<Demux> demux)
void	DemuxDetails.setPoolStep(Linkable<ProcessStep> poolStep)

Method parameters in com.genologics.ri.artifact with type arguments of type Linkable

Modifier and Type	Method	Description
void	Artifact.setArtifactGroups(Collection<? extends Linkable<ArtifactGroup>> links)

Constructors in com.genologics.ri.artifact with parameters of type Linkable

Modifier	Constructor	Description
	ArtifactGroupLink(Linkable<ArtifactGroup> link)
	ControlTypeLink(Linkable<ControlType> link)

Uses of Linkable in com.genologics.ri.artifactgroup

Classes in com.genologics.ri.artifactgroup that implement Linkable

Modifier and Type	Class	Description
class	ArtifactGroupLink	artifactGroup-link is a child element type of artifactGroup and provides a URI linking to the detailed representation of a artifactGroup.

Constructors in com.genologics.ri.artifactgroup with parameters of type Linkable

Modifier	Constructor	Description
	ArtifactGroupLink(Linkable<ArtifactGroup> link)

Uses of Linkable in com.genologics.ri.automation

Classes in com.genologics.ri.automation that implement Linkable

Modifier and Type	Class	Description
class	AutomationLink
class	ProcessTypeLink	Provides links to process types the automation is enabled on.

Methods in com.genologics.ri.automation with parameters of type Linkable

Modifier and Type	Method	Description
void	ProcessTypeLink.setProcessType(Linkable<ProcessType> processType)

Uses of Linkable in com.genologics.ri.configuration

Classes in com.genologics.ri.configuration that implement Linkable

Modifier and Type	Class	Description
class	Field	The detailed representation of the configuration of a user-defined field.
class	FieldLink	Field definition represents a user-defined field configured in the parent entity.
class	Type	The detailed representation of the configuration of a user defined type.
class	TypeDefinition	Type-definition provides a URI linking to the user defined type associated with the user-defined field, if applicable.
class	UdfConfigLink	Udfconfig-link is a child element type of udfs and provides a URI linking to the detailed representation of the configuration for a user defined field.
class	UdtConfigLink	Udtconfig-link is a child element type of udts and provides a URI linking to the detailed representation of the configuration for a user defined type.

Constructors in com.genologics.ri.configuration with parameters of type Linkable

Modifier	Constructor	Description
	FieldLink(Linkable<Field> link)
	TypeDefinition(Linkable<Type> link)

Uses of Linkable in com.genologics.ri.container

Classes in com.genologics.ri.container that implement Linkable

Modifier and Type	Class	Description
class	Container
class	ContainerLink	Container-link is a child element type of containers and provides a URI linking to the detailed representation of a container.
class	ContainerTypeLink	Container-type is a child element of container and provides a URI linking to the detailed representation of the container type that the container is associated with.
class	Placement	Placement is a child element of container and provides a URI linking to the detailed representation of the artifact that is located in a specific well of the container.

Methods in com.genologics.ri.container with parameters of type Linkable

Modifier and Type	Method	Description
void	Container.setContainerType(Linkable<ContainerType> link)

Constructors in com.genologics.ri.container with parameters of type Linkable

Modifier	Constructor	Description
	Container(Linkable<ContainerType> containerType)
	Container(Linkable<ContainerType> containerType, String name)
	ContainerTypeLink(Linkable<ContainerType> link)

Uses of Linkable in com.genologics.ri.containertype

Classes in com.genologics.ri.containertype that implement Linkable

Modifier and Type	Class	Description
class	ContainerType	The detailed representation of a container type.
class	ContainerTypeLink	Container-type-link is a child element type of containers and provides a URI linking to the detailed representation of a container type.

Constructors in com.genologics.ri.containertype with parameters of type Linkable

Modifier	Constructor	Description
	ContainerTypeLink(Linkable<ContainerType> link)

Uses of Linkable in com.genologics.ri.controltype

Classes in com.genologics.ri.controltype that implement Linkable

Modifier and Type	Class	Description
class	ControlType
class	ControlTypeLink	Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.

Uses of Linkable in com.genologics.ri.file

Classes in com.genologics.ri.file that implement Linkable

Modifier and Type	Class	Description
class	ClarityFile	The file element contains information about a file in the system.
class	FileLink	The file-link type provides a URI that links to information about a file in the system.

Methods in com.genologics.ri.file with parameters of type Linkable

Modifier and Type	Method	Description
void	ClarityFile.setAttachedTo(Linkable<?> link)

Uses of Linkable in com.genologics.ri.instrument

Classes in com.genologics.ri.instrument that implement Linkable

Modifier and Type	Class	Description
class	Instrument	The detailed representation of an instrument.
class	InstrumentLink	Instrument-link is a child element type of instruments and provides a URI linking to the detailed representation of an instrument.

Constructors in com.genologics.ri.instrument with parameters of type Linkable

Modifier	Constructor	Description
	InstrumentLink(Linkable<Instrument> link)

Uses of Linkable in com.genologics.ri.instrumenttype

Classes in com.genologics.ri.instrumenttype that implement Linkable

Modifier and Type	Class	Description
class	InstrumentType	An instrument describes properties common to all instruments of that type.
class	InstrumentTypeLink
class	InstrumentTypeProcessType

Uses of Linkable in com.genologics.ri.lab

Classes in com.genologics.ri.lab that implement Linkable

Modifier and Type	Class	Description
class	Lab	The detailed representation of a lab.
class	LabLink	Lab-link is a child element type of labs and provides a URI linking to the detailed representation of a lab.

Constructors in com.genologics.ri.lab with parameters of type Linkable

Modifier	Constructor	Description
	LabLink(Linkable<Lab> link)

Uses of Linkable in com.genologics.ri.permission

Classes in com.genologics.ri.permission that implement Linkable

Modifier and Type	Class	Description
class	Permission
class	PermissionLink

Uses of Linkable in com.genologics.ri.process

Classes in com.genologics.ri.process that implement Linkable

Modifier and Type	Class	Description
class	ArtifactLink	Artifact is a child element of input-output-map and provides a link to an Artifact that was either an input or output of the Process for the input-output-map.
class	ClarityProcess	The detailed representation of a process.
class	InstrumentLink	The instrument element provides a URI to the instrument that is responsible for running the process.
class	ParentProcessLink	Parent-process is a child element of Artifact and provides a URI linking to the Process that created the Artifact.
class	ProcessLink	Process-link is a child element type of process and provides a URI linking to the detailed representation of a process.
class	ProcessTypeLink	Process-type is a child element of process that identifies and provides a URI linking to the detailed representation of the process type that the process is associated with.
class	Technician	Technician is a child element of Process and provides a URI linking to the detailed representation of the technician that ran the Process.

Methods in com.genologics.ri.process with parameters of type Linkable

Modifier and Type	Method	Description
void	InputOutputMap.setInput(Linkable<Artifact> link)
void	ClarityProcess.setInstrument(Linkable<Instrument> link)
void	InputOutputMap.setOutput(Linkable<Artifact> link)
void	ClarityProcess.setProcessType(Linkable<ProcessType> link)
void	ClarityProcess.setTechnician(Linkable<Researcher> link)

Constructors in com.genologics.ri.process with parameters of type Linkable

Modifier	Constructor	Description
	ArtifactLink(Linkable<Artifact> link)
	InputOutputMap(Linkable<Artifact> input, Linkable<Artifact> output)
	InstrumentLink(Linkable<Instrument> link)
	ProcessTypeLink(Linkable<ProcessType> link)
	Technician(Linkable<Researcher> link)

Uses of Linkable in com.genologics.ri.processexecution

Classes in com.genologics.ri.processexecution that implement Linkable

Modifier and Type	Class	Description
class	Input	The input element provides URIs to one or more Artifacts that will be used by the Process.
class	InstrumentLink	The instrument element provides a URI to the instrument that is responsible for running the process.
class	Technician	The technician element provides a URI to the user that is responsible for the Process.

Methods in com.genologics.ri.processexecution with parameters of type Linkable

Modifier and Type	Method	Description
Input	ExecutableInputOutputMap.addInput(Linkable<Artifact> link, QCFlag qc)
void	ExecutableProcess.setInstrument(Linkable<Instrument> link)
void	ExecutableProcess.setTechnician(Linkable<Researcher> link)
protected void	ArtifactBase.updateQCFlag(Linkable<Artifact> link)

Method parameters in com.genologics.ri.processexecution with type arguments of type Linkable

Modifier and Type	Method	Description
void	ExecutableInputOutputMap.setInputs(Collection<? extends Linkable<Artifact>> links)

Constructors in com.genologics.ri.processexecution with parameters of type Linkable

Modifier	Constructor	Description
	ExecutableProcess(String processType, Linkable<Researcher> technician)
	Input(Linkable<Artifact> link)
	InstrumentLink(Linkable<Instrument> link)
	Technician(Linkable<Researcher> link)

Uses of Linkable in com.genologics.ri.processtemplate

Classes in com.genologics.ri.processtemplate that implement Linkable

Modifier and Type	Class	Description
class	InstrumentLink	The instrument is a child element of process-template that provides a URI to the instrument that is responsible for running a Process created using this Process Template.
class	ProcessTemplate	The detailed representation of a Process Template.
class	ProcessTemplateLink	process-template-link is a child element type of Process Templates and provides a URI linking to the detailed representation of a Process Template.
class	ProcessTypeLink	Process-type is a child element of process-template that identifies and provides a URI linking to the detailed representation of the Process Type that the Process Template is associated with.
class	Technician	Technician is a child element of process-template and provides a URI linking to the detailed representation of the technician that is configured to run a Process created using this Process Template.

Constructors in com.genologics.ri.processtemplate with parameters of type Linkable

Modifier	Constructor	Description
	InstrumentLink(Linkable<Instrument> link)
	ProcessTemplateLink(Linkable<ProcessTemplate> link)
	ProcessTypeLink(Linkable<ProcessType> link)
	Technician(Linkable<Researcher> realResearcher)

Uses of Linkable in com.genologics.ri.processtype

Classes in com.genologics.ri.processtype that implement Linkable

Modifier and Type	Class	Description
class	ContainerTypeLink
class	ControlTypeLink
class	ProcessType	The process-type element contains the XML representation of a type of process configured in the system.
class	ProcessTypeLink	Process-type-link is a child element type of process types and provides a URI linking to the detailed representation of a process type.
class	ReagentKitLink	Reagent-kit-link is a child element type of reagentKits and provides a URI linking to the detailed representation of a ReagentKit.
class	TypeDefinition	Type-definition is a child element of process type providing a URI linking to the configuration of a user-defined type for the process type.

Methods in com.genologics.ri.processtype with parameters of type Linkable

Modifier and Type	Method	Description
TypeDefinition	ProcessType.addTypeDefinition(Linkable<Field> link)

Constructors in com.genologics.ri.processtype with parameters of type Linkable

Modifier	Constructor	Description
	ProcessTypeLink(Linkable<ProcessType> link)
	TypeDefinition(Linkable<Field> link)

Uses of Linkable in com.genologics.ri.project

Classes in com.genologics.ri.project that implement Linkable

Modifier and Type	Class	Description
class	Project	The detailed representation of a Project.
class	ProjectLink	Project-link is a child element type of projects and provides a URI linking to the detailed representation of a project.
class	ResearcherLink	Researcher is a child element of Project and provides a URI linking to the detailed representation of the Researcher for the Project.

Methods in com.genologics.ri.project with parameters of type Linkable

Modifier and Type	Method	Description
void	Project.setResearcher(Linkable<Researcher> link)

Constructors in com.genologics.ri.project with parameters of type Linkable

Modifier	Constructor	Description
	ResearcherLink(Linkable<Researcher> link)

Uses of Linkable in com.genologics.ri.protocolconfiguration

Classes in com.genologics.ri.protocolconfiguration that implement Linkable

Modifier and Type	Class	Description
class	Protocol	Detailed representation of a protocol.
class	ProtocolLink

Constructors in com.genologics.ri.protocolconfiguration with parameters of type Linkable

Modifier	Constructor	Description
	ProtocolLink(Linkable<Protocol> link)

Uses of Linkable in com.genologics.ri.queue

Classes in com.genologics.ri.queue that implement Linkable

Modifier and Type	Class	Description
class	ArtifactLink
class	Queue	The representation of a queue.

Uses of Linkable in com.genologics.ri.reagentkit

Classes in com.genologics.ri.reagentkit that implement Linkable

Modifier and Type	Class	Description
class	ReagentKit	The detailed representation of a reagent kit.
class	ReagentKitLink	Reagent-Kit-Link is a child element type of reagent kits and provides a URI linking to the detailed representation of a reagent kit.

Constructors in com.genologics.ri.reagentkit with parameters of type Linkable

Modifier	Constructor	Description
	ReagentKitLink(Linkable<ReagentKit> link)

Uses of Linkable in com.genologics.ri.reagentlot

Classes in com.genologics.ri.reagentlot that implement Linkable

Modifier and Type	Class	Description
class	ReagentKitLink	Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.
class	ReagentLot	The detailed representation of a Reagent Lot
class	ReagentLotLink	Reagent-lot-link is a child element type of Reagent Lots and provides a URI linking to the detailed representation of a Reagent Lot.
class	ResearcherLink	Researcher is a child element of the reagent lot.

Methods in com.genologics.ri.reagentlot with parameters of type Linkable

Modifier and Type	Method	Description
void	ReagentLot.setCreatedBy(Linkable<Researcher> createdBy)
void	ReagentLot.setLastModifiedBy(Linkable<Researcher> lastModifiedBy)
void	ReagentLot.setReagentKit(Linkable<ReagentKit> reagentKit)

Constructors in com.genologics.ri.reagentlot with parameters of type Linkable

Modifier	Constructor	Description
	ReagentKitLink(Linkable<ReagentKit> link)
	ResearcherLink(Linkable<Researcher> link)

Uses of Linkable in com.genologics.ri.reagenttype

Classes in com.genologics.ri.reagenttype that implement Linkable

Modifier and Type	Class	Description
class	ReagentType	The detailed representation of a reagent type.
class	ReagentTypeLink	Reagent-type-link is a child element type of reagent types and provides a URI linking to the detailed representation of a reagent type.

Constructors in com.genologics.ri.reagenttype with parameters of type Linkable

Modifier	Constructor	Description
	ReagentTypeLink(Linkable<ReagentType> link)

Uses of Linkable in com.genologics.ri.researcher

Classes in com.genologics.ri.researcher that implement Linkable

Modifier and Type	Class	Description
class	LabLink	Lab is a child element of researcher and provides a URI linking to the detailed representation of the lab for the researcher.
class	Researcher	The detailed representation of a researcher.
class	ResearcherLink	Researcher-link is a child element type of researchers and provides a URI linking to the detailed representation of a researcher.
class	Role	The role element defines a researcher's level of access in the system.

Methods in com.genologics.ri.researcher with parameters of type Linkable

Modifier and Type	Method	Description
void	Researcher.setLab(Linkable<Lab> link)

Constructors in com.genologics.ri.researcher with parameters of type Linkable

Modifier	Constructor	Description
	LabLink(Linkable<Lab> link)
	ResearcherLink(Linkable<Researcher> link)
	Role(Linkable<Role> link)

Uses of Linkable in com.genologics.ri.role

Classes in com.genologics.ri.role that implement Linkable

Modifier and Type	Class	Description
class	PermissionLink	Permission-link is a child element type of permissions and provides a URI linking to the detailed representation of a Permission.
class	ResearcherLink	Researcher-link is a child element type of researchers and provides a URI linking to the detailed representation of a researcher.
class	Role	The detailed representation of a Role
class	RoleLink	Role-link is a child element type of roles and provides a URI linking to the detailed representation of a Role.

Uses of Linkable in com.genologics.ri.routing

Classes in com.genologics.ri.routing that implement Linkable

Modifier and Type	Class	Description
class	ArtifactLink

Methods in com.genologics.ri.routing with parameters of type Linkable

Modifier and Type	Method	Description
void	ExtArtifactAssignments.addArtifact(Linkable<Artifact> artifact)
void	ExtArtifactAssignments.setStage(Linkable<Stage> stage)
void	ExtArtifactAssignments.setWorkflow(Linkable<Workflow> workflow)

Method parameters in com.genologics.ri.routing with type arguments of type Linkable

Modifier and Type	Method	Description
void	ExtArtifactAssignments.addAll(Collection<? extends Linkable<Artifact>> links)

Constructors in com.genologics.ri.routing with parameters of type Linkable

Modifier	Constructor	Description
	ArtifactLink(Linkable<Artifact> link)

Uses of Linkable in com.genologics.ri.sample

Classes in com.genologics.ri.sample that implement Linkable

Modifier and Type	Class	Description
class	ArtifactLink	Artifact is a child element of Sample and provides a URI linking to the detailed representation of the artifact for the Sample.
class	ControlTypeLink	Control Type provides a name and a URI linking to the detailed representation of the Control Type associated with the Sample.
class	ProjectLink	Project is a child element of Sample and provides a URI linking to the detailed representation of the Project for the Sample.
class	Sample	The detailed representation of a sample.
class	SampleLink	Sample-link is a child element type of samples and provides a URI linking to the detailed representation of a sample.
class	Submitter	Submitter is a child element of Sample and provides a URI linking to the detailed representation of the submitter for the Sample.

Methods in com.genologics.ri.sample with parameters of type Linkable

Modifier and Type	Method	Description
void	SampleBase.setControlType(Linkable<ControlType> controlType)
Submitter	SampleBase.setSubmitter(Linkable<Researcher> link)

Constructors in com.genologics.ri.sample with parameters of type Linkable

Modifier	Constructor	Description
	ControlTypeLink(Linkable<ControlType> link)
	Submitter(Linkable<Researcher> link)

Uses of Linkable in com.genologics.ri.stage

Classes in com.genologics.ri.stage that implement Linkable

Modifier and Type	Class	Description
class	ProtocolLink	Protocol link for the stage.
class	ProtocolStepLink	Protocol Step link for the stage.
class	Stage	The detailed representation of a stage.
class	WorkflowLink	Workflow link for the stage.

Methods in com.genologics.ri.stage with parameters of type Linkable

Modifier and Type	Method	Description
void	Stage.setProtocol(Linkable<Protocol> protocol)
void	Stage.setStep(Linkable<ProtocolStep> step)
void	Stage.setWorkflow(Linkable<Workflow> workflow)

Constructors in com.genologics.ri.stage with parameters of type Linkable

Modifier	Constructor	Description
	ProtocolLink(Linkable<Protocol> link)
	ProtocolStepLink(Linkable<ProtocolStep> link)
	WorkflowLink(Linkable<Workflow> link)

Uses of Linkable in com.genologics.ri.step

Classes in com.genologics.ri.step that implement Linkable

Modifier and Type	Class	Description
class	Actions
class	ActionsLink	Identifies the resource that represents the actions applied or to be applied by the step.
class	ArtifactLink	Artifact is a child element of input-output-map and provides a link to an Artifact that was either an input or output of the Step for the input-output-map.
class	AutomaticNextStepLink	Identifies the resource that represents the step that was automatically begun when the "Automatically start Next Step" option is enabled in a step's configuration.
class	ContainerLink	Provides a URI linking to a selected container to be used for placement.
class	CreationInput	Typically, provides a URI linking to the input artifact.
class	EscalatedArtifact	Sample next action or step.
class	Input	Provides input URI links.
class	InstrumentLink	The instrument element provides a URI to the selected instrument for the step.
class	NextAction	Sample next action or step.
class	Output	Provides a URI linking to the output artifact and reagent label.
class	OutputPlacement	Provides a URI linking to the output artifact and container placement.
class	Placements	The detailed representation of a step's output artifact container placements
class	PlacementsLink	Identifies the resource that represents the output placements for the step.
class	Pools	The detailed representation of a step's pooled inputs.
class	PoolsLink	Identifies the resource that represents the pools added by the step.
class	ProcessStep	The detailed representation of a step.
class	ProgramStatus	The current EPP status for a step (supports automatically triggered programs only).
class	ProgramStatusLink	Identifies the resource that represents the program status for the step.
class	ReagentLotLink	Provides a URI linking to the reagent lot details.
class	ReagentLots	The list representation of a step's reagent lots.
class	ReagentLotsLink	Identifies the resource that represents the reagent lots for the step.
class	Reagents	The detailed representation of a step's output artifact reagents.
class	ReagentsLink	Identifies the resource that represents the reagents added by the step.
class	SharedResultFile	The file element describes a shared result file output that will be displayed in the step-setup view.
class	StepConfiguration	Identifies the configuration information for the step run.
class	StepDetails
class	StepDetailsLink	Identifies the resource that represents the details for the step.
class	StepSetup
class	StepSetupLink	Identifies the resource that represents the setup for the step.
class	UserLink	Describes a user as required in the context of step escalations.

Methods in com.genologics.ri.step with parameters of type Linkable

Modifier and Type	Method	Description
Input	Pools.addAvailableInput(Linkable<Artifact> artifact)
EscalatedArtifact	Escalation.addEscalatedArtifact(Linkable<Artifact> link)
Input	PooledInputs.addInput(Linkable<Artifact> artifact)
CreationInput	StepCreation.addInput(Linkable<Artifact> artifact, Linkable<ControlType> controlType, Long replicates)
OutputPlacement	Placements.addOutputPlacement(Linkable<Artifact> artifact, Linkable<Container> container, String wellPosition)
PooledInputs	Pools.addPooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName, Linkable<Artifact> outputArtifact)
ContainerLink	Placements.addSelectedContainer(Linkable<Container> container)
void	CreationInput.setArtifact(Linkable<Artifact> a)
void	NextAction.setArtifact(Linkable<Artifact> link)
void	Output.setArtifact(Linkable<Artifact> artifact)
void	OutputPlacement.setArtifact(Linkable<Artifact> artifact)
void	EscalationRequest.setAuthor(Linkable<Researcher> link)
void	EscalationReview.setAuthor(Linkable<Researcher> link)
void	ProcessStep.setAutomaticNextStep(Linkable<ProcessStep> step)
void	StepCreation.setConfiguration(Linkable<ProtocolStep> step)
void	CreationInput.setControlType(Linkable<ControlType> type)
void	ProcessStep.setDetails(Linkable<StepDetails> link)
void	InputOutputMap.setInput(Linkable<Artifact> link)
void	StepDetails.setInstrument(Linkable<Instrument> link)
void	OutputPlacement.setLocation(Linkable<Container> container, String wellPosition)
void	InputOutputMap.setOutput(Linkable<Artifact> link)
void	PooledInputs.setOutputArtifact(Linkable<Artifact> artifact)
void	ProcessStep.setPlacements(Linkable<Placements> placements)
void	ProcessStep.setPools(Linkable<Pools> pools)
void	ProcessStep.setProgramStatus(Linkable<ProgramStatus> programStatus)
void	StepConfiguration.setProtocolStep(Linkable<ProtocolStep> protocolStep)
void	ProcessStep.setReagentLots(Linkable<ReagentLots> link)
void	ProcessStep.setReagents(Linkable<Reagents> reagents)
void	EscalationRequest.setReviewer(Linkable<Researcher> link)
void	NextAction.setReworkStep(Linkable<ProtocolStep> step)
void	ProcessStep.setSetup(Linkable<StepSetup> link)
void	NextAction.setStep(Linkable<ProtocolStep> step)
void	Placements.setStep(Linkable<ProcessStep> step)

Method parameters in com.genologics.ri.step with type arguments of type Linkable

Modifier and Type	Method	Description
PooledInputs	Pools.addPooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName, Linkable<Artifact> outputArtifact)
void	PooledInputs.setInputArtifacts(Collection<? extends Linkable<Artifact>> artifacts)

Constructors in com.genologics.ri.step with parameters of type Linkable

Modifier	Constructor	Description
	ActionsLink(Linkable<Actions> link)
	ArtifactLink(Linkable<Artifact> link)
	AutomaticNextStepLink(Linkable<ProcessStep> link)
	ContainerLink(Linkable<Container> link)
	CreationInput(Linkable<Artifact> artifact)
	CreationInput(Linkable<Artifact> artifact, Linkable<ControlType> controlType)
	CreationInput(Linkable<Artifact> artifact, Linkable<ControlType> controlType, Long replicates)
	EscalatedArtifact(Linkable<Artifact> link)
	Input(Linkable<Artifact> link)
	InputOutputMap(Linkable<Artifact> input, Linkable<Artifact> output)
	InstrumentLink(Linkable<Instrument> link)
	NextAction(Linkable<Artifact> link)
	NextAction(Linkable<Artifact> link, ActionType action)
	NextAction(Linkable<Artifact> link, ActionType action, Linkable<ProtocolStep> nextStep)
	NextAction(URI artifactUri, ActionType action, Linkable<ProtocolStep> nextStep)
	OutputPlacement(Linkable<Artifact> artifact)
	OutputPlacement(Linkable<Artifact> artifact, LimsEntityLinkable<Container> container, String wellPosition)
	OutputPlacement(Linkable<Artifact> artifact, Linkable<Container> container, String wellPosition)
	PlacementsLink(Linkable<Placements> placements)
	PooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName, Linkable<Artifact> outputArtifact)
	PoolsLink(Linkable<Pools> pools)
	ProgramStatusLink(Linkable<ProgramStatus> link)
	ReagentLotsLink(Linkable<ReagentLots> link)
	ReagentsLink(Linkable<Reagents> link)
	StepConfiguration(Linkable<ProtocolStep> step)
	StepCreation(Linkable<ProtocolStep> step)
	StepDetailsLink(Linkable<StepDetails> link)
	StepSetupLink(Linkable<StepSetup> link)
	UserLink(Linkable<Researcher> link)

Constructor parameters in com.genologics.ri.step with type arguments of type Linkable

Modifier	Constructor	Description
	PooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName)
	PooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName, Linkable<Artifact> outputArtifact)

Uses of Linkable in com.genologics.ri.stepconfiguration

Classes in com.genologics.ri.stepconfiguration that implement Linkable

Modifier and Type	Class	Description
class	ControlTypeLink	Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.
class	NextStep	List of step transitions including the URI allowing access to the specific next step
class	ProcessTypeLink	Process-type is a child element that provides a URI linking to the detailed representation of the process type that the step is associated with.
class	ProtocolStep	Detailed representation of a Step
class	ReagentKitLink	Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.

Methods in com.genologics.ri.stepconfiguration with parameters of type Linkable

Modifier and Type	Method	Description
ControlTypeLink	ProtocolStep.addPermittedControlType(Linkable<ControlType> controlType)
ReagentKitLink	ProtocolStep.addRequiredReagentKit(Linkable<ReagentKit> kit)
void	NextStep.setNextStep(Linkable<ProtocolStep> step)
void	ProtocolStep.setProcessType(Linkable<ProcessType> processType)

Constructors in com.genologics.ri.stepconfiguration with parameters of type Linkable

Modifier	Constructor	Description
	ControlTypeLink(Linkable<ControlType> link)
	ProcessTypeLink(Linkable<ProcessType> link)
	ReagentKitLink(Linkable<ReagentKit> link)

Uses of Linkable in com.genologics.ri.workflowconfiguration

Classes in com.genologics.ri.workflowconfiguration that implement Linkable

Modifier and Type	Class	Description
class	ProtocolLink	Protocol-link is a child element type of workflow and provides a URI linking to the detailed representation of a protocol.
class	StageLink	The detailed representation of a Stage (the portion of a workflow to which samples can be associated in order to be queued)
class	Workflow	The detailed representation of a Workflow.
class	WorkflowLink	Workflow-link is a child element type of workflows and provides a URI linking to the detailed representation of a workflow.

Methods in com.genologics.ri.workflowconfiguration with parameters of type Linkable

Modifier and Type	Method	Description
ProtocolLink	Workflow.addProtocol(Linkable<Protocol> protocol)
StageLink	Workflow.addStage(Linkable<Stage> stage)

Constructors in com.genologics.ri.workflowconfiguration with parameters of type Linkable

Modifier	Constructor	Description
	ProtocolLink(Linkable<Protocol> link)
	StageLink(Linkable<Stage> link)
	WorkflowLink(Linkable<Workflow> link)

Uses of Linkable in org.cruk.clarity.api

Methods in org.cruk.clarity.api with parameters of type Linkable

Modifier and Type	Method	Description
void	ClarityAPI.deleteAndRemoveFile(Linkable<ClarityFile> file)	Delete a file from the file store and remove its record from the LIMS.
void	ClarityAPI.downloadFile(Linkable<ClarityFile> file, OutputStream resultStream)	Download the given file from its source.
List<LimsEntityLink<Artifact>>	ClarityAPI.listQueue(Linkable<ProtocolStep> protocolStep)	List the artifacts in the queue for the given protocol step.
List<LimsEntityLink<Artifact>>	ClarityAPI.listQueue(Linkable<ProtocolStep> protocolStep, Map<String,?> searchTerms)	List the artifacts in the queue for the given protocol step, additionally filtering using the parameters available for the "queues" end point.

Uses of Linkable in org.cruk.clarity.api.impl

Methods in org.cruk.clarity.api.impl with parameters of type Linkable

Modifier and Type	Method	Description
void	ClarityAPIImpl.deleteAndRemoveFile(Linkable<ClarityFile> file)	Delete a file from the file store and remove its record from the LIMS.
void	ClarityAPIImpl.downloadFile(Linkable<ClarityFile> file, OutputStream resultStream)	Download the given file from its source.
List<LimsEntityLink<Artifact>>	ClarityAPIImpl.listQueue(Linkable<ProtocolStep> protocolStep)	List the artifacts in the queue for the given protocol step.
List<LimsEntityLink<Artifact>>	ClarityAPIImpl.listQueue(Linkable<ProtocolStep> protocolStep, Map<String,?> searchTerms)	List the artifacts in the queue for the given protocol step, additionally filtering using the parameters available for the "queues" end point.

Method parameters in org.cruk.clarity.api.impl with type arguments of type Linkable

Modifier and Type	Method	Description
protected Links	ClarityAPIImpl.toLinks(Collection<? extends Linkable<?>> entityLinks, boolean stripState)	Create a Links object containing the URIs of the link objects given.