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	Provides JAXB bindings for artifacts in the Genologics REST API.
com.genologics.ri.artifactgroup	Entities for artifact groups in the Clarity system.
com.genologics.ri.automation	Entities for automation resources in the Clarity system.
com.genologics.ri.configuration	Entities for system configuration in the Clarity system.
com.genologics.ri.container	Container entity and support classes for the Clarity REST API.
com.genologics.ri.containertype	Entities for container type definitions in the Clarity system.
com.genologics.ri.controltype	Entities for control types in the Clarity LIMS system.
com.genologics.ri.file	Entities for file resources in the Clarity system.
com.genologics.ri.globaltoken	Illumina have said that the types in this package are not actually released, and there's nothing in Clarity that uses them.
com.genologics.ri.instrument	Entities for instrument resources in the Clarity system.
com.genologics.ri.instrumenttype	Entities for instrument type definitions in the Clarity system.
com.genologics.ri.lab	Provides classes for representing and managing laboratory entities in the Clarity LIMS system.
com.genologics.ri.permission	Entities for user permissions in the Clarity system.
com.genologics.ri.process	Entities for processes executed in the Clarity system.
com.genologics.ri.processexecution	Entities for process execution in the Clarity system.
com.genologics.ri.processtemplate	Entities for process templates in the Clarity system.
com.genologics.ri.processtype	Entities for process type definitions in the Clarity system.
com.genologics.ri.project	Project entity and supporting classes for the Clarity REST API.
com.genologics.ri.protocolconfiguration	Provides JAXB bindings for the protocol configuration domain model.
com.genologics.ri.queue	Entities for work queues in the Clarity system.
com.genologics.ri.reagentkit	Provides JAXB binding classes for the Clarity REST API reagent kit entity and its related components.
com.genologics.ri.reagentlot
com.genologics.ri.reagenttype	Entities for reagent type definitions in the Clarity system.
com.genologics.ri.researcher	Provides classes for representing researchers in the Clarity LIMS system.
com.genologics.ri.role	Provides JAXB binding classes for the Clarity REST API role entity and its related components.
com.genologics.ri.routing	Provides JAXB binding classes for the Clarity REST API routing entity and its related components.
com.genologics.ri.sample	Provides classes for sample entities in the Clarity LIMS API.
com.genologics.ri.savedquery	Entities for saved queries in the Clarity system.
com.genologics.ri.stage	Entities for workflow stages in the Clarity system.
com.genologics.ri.step	Entities for workflow steps in the Clarity system.
com.genologics.ri.stepconfiguration	Entities for step configuration in the Clarity system.
com.genologics.ri.workflowconfiguration	Entities for workflow configuration in the Clarity system.
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	LimsEntityLinkBase<E extends LimsEntity<E>>	Helper base class for LimsEntityLink implementations extending from LimsLinkBase.
class	LimsLinkBase<E extends Locatable>	Helper base class for LimsLink implementations that implements LimsLinkBase.hashCode() and LimsLinkBase.equals(Object) to consider links that point to the same entities as equivalent.
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)	Adds a linkable object as a link to this collection.

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

Modifier	Constructor	Description
	ContainerLink(Linkable<Container> link)	Constructor from a linkable container.
	Link(Linkable<?> linkable)	Constructor from a linkable object.
	Location(Linkable<Container> container, String position)	Constructor with container and 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	DemuxArtifact	Details of an individual artifact that is part of a pooled artifact.
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	Link to a source artifact for demultiplexing.
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)	Adds an artifact group to this artifact.
SampleLink	Artifact.addSample(Linkable<Sample> linkable)	Adds a sample to this artifact.
void	DemuxLink.setArtifact(Linkable<DemuxArtifact> artifact)	Sets the artifact from a Linkable.
void	DemuxSourceArtifact.setArtifact(Linkable<Artifact> artifact)	Sets the artifact from a Linkable.
void	Artifact.setControlType(Linkable<ControlType> link)	Sets the control type for this artifact.
void	Artifact.setDemux(Linkable<Demux> demux)	Sets the demultiplexing information for this artifact.
void	DemuxDetails.setPoolStep(Linkable<ProcessStep> poolStep)	Sets the pool step from a Linkable.

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)	Sets the artifact groups this artifact belongs to.

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

Modifier	Constructor	Description
	ArtifactGroupLink(Linkable<ArtifactGroup> link)	Constructor from a Linkable.
	ArtifactLink(Linkable<Artifact> link)	Constructor from a Linkable.
	ControlTypeLink(Linkable<ControlType> link)	Constructor from a Linkable.
	DemuxArtifactSample(Linkable<Sample> link)	Constructor from a Linkable.
	DemuxLink(Linkable<DemuxArtifact> link)	Constructor from a Linkable.
	DemuxSourceArtifact(Linkable<Artifact> link)	Constructor from a Linkable.
	ParentProcessLink(Linkable<ClarityProcess> link)	Constructor from a Linkable.
	PoolStep(Linkable<ProcessStep> step)	Constructor from a Linkable.
	SampleLink(Linkable<Sample> link)	Constructor from a Linkable.
	WorkflowStage(Linkable<Stage> link)	Constructor from a Linkable.

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)	Constructs a link from a Linkable object.

Uses of Linkable in com.genologics.ri.automation

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

Modifier and Type	Class	Description
class	Automation	The automation element integrates the process with the Automation Worker (previously called External Program Plugin or EPP).
class	AutomationLink	A link to an Automation entity.
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)	Sets the process type from a linkable.

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

Modifier	Constructor	Description
	AutomationLink(Linkable<Automation> link)	Constructor from a Linkable.
	ProcessTypeLink(Linkable<ProcessType> link)	Constructor from a Linkable.

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)	Constructor for creating a FieldLink from a Linkable object.
	TypeDefinition(Linkable<Type> type)	Constructor for creating a TypeDefinition from a Linkable object.

Uses of Linkable in com.genologics.ri.container

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

Modifier and Type	Class	Description
class	Container	Container entity representing a physical container in the Clarity LIMS.
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)	Sets the container type from a linkable.

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

Modifier	Constructor	Description
	Container(Linkable<ContainerType> containerType)	Constructor with container type link.
	Container(Linkable<ContainerType> containerType, String name)	Constructor with container type link and name.
	ContainerLink(Linkable<Container> link)	Constructor from a linkable container.
	ContainerTypeLink(Linkable<ContainerType> link)	Constructor from a linkable container type.

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)	Constructor for creating a container type link from a linkable object.

Uses of Linkable in com.genologics.ri.controltype

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

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

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

Modifier	Constructor	Description
	ControlTypeLink(Linkable<ControlType> link)	Constructs a control type link from a linkable object.

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)	Sets the resource that this file is attached to.

Uses of Linkable in com.genologics.ri.globaltoken

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

Modifier and Type	Class	Description
class	GlobalToken	Clarity global token.
class	GlobalTokenLink	global-token-link is a child element type of global tokens and provides a URI linking to the detailed representation of a global token.

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)	Constructor from a linkable instrument.

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	Instrument-type-link provides a URI linking to the detailed representation of an instrument type.
class	InstrumentTypeProcessType	Process type link for instrument types.

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

Modifier	Constructor	Description
	InstrumentTypeLink(Linkable<InstrumentType> link)	Constructor from a linkable instrument type.
	InstrumentTypeProcessType(Linkable<ProcessType> link)	Constructor from a linkable process type.

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)	Constructs a new LabLink instance from a linkable object.

Uses of Linkable in com.genologics.ri.permission

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

Modifier and Type	Class	Description
class	Permission	The detailed representation of a permission.
class	PermissionLink	Permission-link provides a URI linking to the detailed representation of a permission.

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)	Sets the input from a linkable artifact.
void	ClarityProcess.setInstrument(Linkable<Instrument> link)	Sets the instrument from a linkable object.
void	InputOutputMap.setOutput(Linkable<Artifact> link)	Sets the output from a linkable artifact.
void	ClarityProcess.setProcessType(Linkable<ProcessType> link)	Sets the process type from a linkable object.
void	ClarityProcess.setTechnician(Linkable<Researcher> link)	Sets the technician from a linkable researcher.

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

Modifier	Constructor	Description
	ArtifactLink(Linkable<Artifact> link)	Constructor from a linkable object.
	InputOutputMap(Linkable<Artifact> input, Linkable<Artifact> output)	Constructor with input and output linkable artifacts.
	InstrumentLink(Linkable<Instrument> link)	Constructor from a linkable object.
	ParentProcessLink(Linkable<ClarityProcess> link)	Constructor from a linkable object.
	ProcessLink(Linkable<ClarityProcess> link)	Constructor from a linkable object.
	ProcessTypeLink(Linkable<ProcessType> link)	Constructor from a linkable object.
	Technician(Linkable<Researcher> link)	Constructor from a linkable object.

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)	Adds an input with a QC flag to the input list.
void	ExecutableProcess.setInstrument(Linkable<Instrument> link)	Sets the instrument from an instrument link.
void	ExecutableProcess.setTechnician(Linkable<Researcher> link)	Sets the technician from a researcher link.
protected void	ArtifactBase.updateQCFlag(Linkable<Artifact> link)	Updates the QC flag from a linkable artifact.

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)	Sets the inputs from a collection of artifact links.

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

Modifier	Constructor	Description
	ExecutableProcess(String processType, Linkable<Researcher> technician)	Constructor with process type and technician.
	Input(Linkable<Artifact> link)	Constructor from a linkable artifact.
	InstrumentLink(Linkable<Instrument> link)	Constructor from a linkable instrument.
	Technician(Linkable<Researcher> link)	Constructor from a linkable researcher.

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)	Constructor from a linkable instrument.
	ProcessTemplateLink(Linkable<ProcessTemplate> link)	Constructor from a linkable process template.
	ProcessTypeLink(Linkable<ProcessType> link)	Constructor from a linkable process type.
	Technician(Linkable<Researcher> link)	Constructs a new Technician from a linkable researcher object.

Uses of Linkable in com.genologics.ri.processtype

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

Modifier and Type	Class	Description
class	ContainerTypeLink	Link to a container type within a process type configuration.
class	ControlTypeLink	Link to a control type within a process type configuration.
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)	Adds a type definition for the specified field.

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

Modifier	Constructor	Description
	ContainerTypeLink(Linkable<ContainerType> link)	Constructs a new container type link from a linkable object.
	ControlTypeLink(Linkable<ControlType> link)	Constructs a new control type link from a linkable object.
	ProcessTypeLink(Linkable<ProcessType> link)	Constructs a new process type link from a linkable object.
	ReagentKitLink(Linkable<ReagentKit> link)	Constructs a new reagent kit link from a linkable object.
	TypeDefinition(Linkable<Field> field)	Constructs a new type definition from a linkable field.

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)	Set the researcher associated with the project.

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

Modifier	Constructor	Description
	ProjectLink(Linkable<Project> link)	Constructor for ProjectLink from a Linkable.
	ResearcherLink(Linkable<Researcher> link)	Constructor for ResearcherLink from a Linkable.

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	Link to a protocol configuration.

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

Modifier	Constructor	Description
	ProtocolLink(Linkable<Protocol> link)	Constructor from a linkable object.

Uses of Linkable in com.genologics.ri.queue

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

Modifier and Type	Class	Description
class	ArtifactLink	Artifact-Link provides a URI linking to the detailed representation of an artifact in a queue.

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

Modifier	Constructor	Description
	ArtifactLink(Linkable<Artifact> link)	Constructor from a Linkable.

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)	Constructor from a Linkable.

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	Represents a reagent lot in the Clarity LIMS system.
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)	Sets the researcher who created this lot.
void	ReagentLot.setLastModifiedBy(Linkable<Researcher> lastModifiedBy)	Sets the researcher who last modified this lot.
void	ReagentLot.setReagentKit(Linkable<ReagentKit> reagentKit)	Sets the reagent kit for this lot.

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

Modifier	Constructor	Description
	ReagentKitLink(Linkable<ReagentKit> link)	Constructor from a linkable reagent kit.
	ReagentLotLink(Linkable<ReagentLot> link)	Constructor from a linkable reagent lot.
	ResearcherLink(Linkable<Researcher> link)	Constructor from a linkable researcher.

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)	Constructor from a Linkable object.

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)	Sets the link to the researcher's lab.

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

Modifier	Constructor	Description
	LabLink(Linkable<Lab> link)	Constructor from a linkable object.
	ResearcherLink(Linkable<Researcher> link)	Constructor from a linkable object.
	Role(Linkable<Role> link)	Constructor from a linkable object.

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.

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

Modifier	Constructor	Description
	ResearcherLink(Linkable<Researcher> link)	Constructor from a Linkable.

Uses of Linkable in com.genologics.ri.routing

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

Modifier and Type	Class	Description
class	ArtifactLink	Link to an artifact for routing purposes.

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

Modifier and Type	Method	Description
void	ExtArtifactAssignments.addArtifact(Linkable<Artifact> artifact)	Adds an artifact to the list.
void	ExtArtifactAssignments.setStage(Linkable<Stage> stage)	Sets the stage from a Linkable.
void	ExtArtifactAssignments.setWorkflow(Linkable<Workflow> workflow)	Sets the workflow from a Linkable.

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)	Adds all artifacts from a collection to the list.

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

Modifier	Constructor	Description
	ArtifactLink(Linkable<Artifact> link)	Constructor from a Linkable.

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)	Sets the control type for this sample.
Submitter	SampleBase.setSubmitter(Linkable<Researcher> link)	Sets the submitter for this sample.

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

Modifier	Constructor	Description
	ArtifactLink(Linkable<Artifact> link)	Constructor for an artifact link from a linkable artifact.
	ControlTypeLink(Linkable<ControlType> link)	Constructor for a control type link from a linkable control type.
	ProjectLink(Linkable<Project> link)	Constructor for a project link from a linkable project.
	SampleLink(Linkable<Sample> link)	Constructor for a sample link from a linkable sample.
	Submitter(Linkable<Researcher> link)	Constructor for a submitter from a linkable researcher.

Uses of Linkable in com.genologics.ri.savedquery

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

Modifier and Type	Class	Description
class	SavedQuery	Represents a saved query in the Clarity LIMS system.
class	SavedQueryLink	Link to a saved query entity.

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 a stage in a workflow.
class	ProtocolStepLink	Protocol step link for a stage in a workflow.
class	Stage	The detailed representation of a workflow stage.
class	WorkflowLink	Workflow link for a stage.

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

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

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

Modifier	Constructor	Description
	ProtocolLink(Linkable<Protocol> link)	Constructor from a linkable protocol object.
	ProtocolStepLink(Linkable<ProtocolStep> link)	Constructor from a linkable protocol step object.
	WorkflowLink(Linkable<Workflow> link)	Constructor from a linkable workflow object.

Uses of Linkable in com.genologics.ri.step

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

Modifier and Type	Class	Description
class	Actions	Represents actions applied or to be applied by a step in the workflow.
class	ActionsLink	Identifies the resource that represents the actions applied or to be applied by the step.
class	Arrangements	The detailed representation of a step's output container Tube Rack arrangements only for an Add Label Step.
class	ArrangementsLink	Identifies the resource that represents the arrangements (if any) for 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	OutputArrangement	Provides a URI linking to the output container and Tube Rack arrangement.
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	Represents the detailed view of a step, including configuration, input/output mappings, user-defined fields, and associated resources.
class	StepDetailsLink	Identifies the resource that represents the details for the step.
class	StepSetup	Represents the setup configuration for a step, including files and configuration settings.
class	StepSetupLink	Identifies the resource that represents the setup for the step.
class	Technician	Technician is a child element of Step and provides a URI linking to the detailed representation of the technician that ran 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)	Creates and adds an available input from an artifact.
EscalatedArtifact	Escalation.addEscalatedArtifact(Linkable<Artifact> link)	Adds an escalated artifact to the list from a linkable artifact.
Input	PooledInputs.addInput(Linkable<Artifact> artifact)	Creates and adds an input from an artifact.
CreationInput	StepCreation.addInput(Linkable<Artifact> artifact, Linkable<ControlType> controlType, Long replicates)	Creates and adds an input to the step.
OutputPlacement	Placements.addOutputPlacement(Linkable<Artifact> artifact, Linkable<Container> container, String wellPosition)	Creates and adds an output placement.
PooledInputs	Pools.addPooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName, Linkable<Artifact> outputArtifact)	Creates and adds a pooled input group.
ContainerLink	Placements.addSelectedContainer(Linkable<Container> container)	Adds a selected container.
void	ProcessStep.setArrangements(Linkable<Arrangements> arrangements)	Sets the link to the arrangements associated with this step.
void	CreationInput.setArtifact(Linkable<Artifact> a)	Sets the artifact.
void	NextAction.setArtifact(Linkable<Artifact> link)	Sets the artifact.
void	Output.setArtifact(Linkable<Artifact> artifact)	Sets the artifact.
void	OutputPlacement.setArtifact(Linkable<Artifact> artifact)	Sets the artifact for this output placement.
void	EscalationRequest.setAuthor(Linkable<Researcher> link)	Sets the author.
void	EscalationReview.setAuthor(Linkable<Researcher> link)	Sets the author.
void	ProcessStep.setAutomaticNextStep(Linkable<ProcessStep> step)	Sets the link to the next step that will be automatically triggered after this step.
void	StepCreation.setConfiguration(Linkable<ProtocolStep> step)	Sets the step configuration from a protocol step link.
void	CreationInput.setControlType(Linkable<ControlType> type)	Sets the control type.
void	ProcessStep.setDetails(Linkable<StepDetails> link)	Sets the link to the details associated with this step.
void	InputOutputMap.setInput(Linkable<Artifact> link)	Sets the input from a linkable artifact.
void	StepDetails.setInstrument(Linkable<Instrument> link)	Sets the instrument from a link.
void	OutputPlacement.setLocation(Linkable<Container> container, String wellPosition)	Sets the location from a container and well position.
void	InputOutputMap.setOutput(Linkable<Artifact> link)	Sets the output from a linkable artifact.
void	PooledInputs.setOutputArtifact(Linkable<Artifact> artifact)	Sets the output artifact.
void	ProcessStep.setPlacements(Linkable<Placements> placements)	Sets the link to the placements associated with this step.
void	ProcessStep.setPools(Linkable<Pools> pools)	Sets the link to the pools associated with this step.
void	ProcessStep.setProgramStatus(Linkable<ProgramStatus> programStatus)	Sets the link to the program status associated with this step.
void	StepConfiguration.setProtocolStep(Linkable<ProtocolStep> protocolStep)	Sets the protocol step from a linkable object.
void	ProcessStep.setReagentLots(Linkable<ReagentLots> link)	Sets the link to the reagent lots associated with this step.
void	ProcessStep.setReagents(Linkable<Reagents> reagents)	Sets the link to the reagents associated with this step.
void	EscalationRequest.setReviewer(Linkable<Researcher> link)	Sets the reviewer.
void	NextAction.setReworkStep(Linkable<ProtocolStep> step)	Sets the rework step.
void	ProcessStep.setSetup(Linkable<StepSetup> link)	Sets the link to the setup associated with this step.
void	NextAction.setStep(Linkable<ProtocolStep> step)	Sets the next step.
void	Placements.setStep(Linkable<ProcessStep> step)	Sets the step from a linkable process step.
void	ProcessStep.setTechnician(Linkable<Researcher> technician)	Sets the technician assigned to this step from a linkable researcher.

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)	Creates and adds a pooled input group.
void	PooledInputs.setInputArtifacts(Collection<? extends Linkable<Artifact>> artifacts)	Sets the input artifacts, replacing any existing inputs.

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

Modifier	Constructor	Description
	ActionsLink(Linkable<Actions> link)	Constructor from a linkable object.
	ArrangementsLink(Linkable<Arrangements> link)	Constructor from a linkable object.
	ArtifactLink(Linkable<Artifact> link)	Constructor from a linkable object.
	AutomaticNextStepLink(Linkable<ProcessStep> link)	Constructor from a linkable object.
	ContainerLink(Linkable<Container> link)	Constructor from a linkable object.
	CreationInput(Linkable<Artifact> artifact)	Constructor from a linkable artifact.
	CreationInput(Linkable<Artifact> artifact, Linkable<ControlType> controlType)	Constructor from a linkable artifact and control type.
	CreationInput(Linkable<Artifact> artifact, Linkable<ControlType> controlType, Long replicates)	Constructor from a linkable artifact, control type, and replicates.
	EscalatedArtifact(Linkable<Artifact> link)	Constructor from a linkable object.
	Input(Linkable<Artifact> link)	Constructor from a linkable object.
	InputOutputMap(Linkable<Artifact> input, Linkable<Artifact> output)	Constructor with linkable input and output artifacts.
	InstrumentLink(Linkable<Instrument> link)	Constructor from a linkable object.
	NextAction(Linkable<Artifact> link)	Constructor from a linkable artifact.
	NextAction(Linkable<Artifact> link, ActionType action)	Constructor from a linkable artifact and action.
	NextAction(Linkable<Artifact> link, ActionType action, Linkable<ProtocolStep> nextStep)	Constructor from a linkable artifact, action, and next step.
	NextAction(URI artifactUri, ActionType action, Linkable<ProtocolStep> nextStep)	Constructor with artifact URI, action, and next step.
	OutputPlacement(Linkable<Artifact> artifact)	Constructor with artifact.
	OutputPlacement(Linkable<Artifact> artifact, LimsEntityLinkable<Container> container, String wellPosition)	Constructor with artifact, container and well position.
	OutputPlacement(Linkable<Artifact> artifact, Linkable<Container> container, String wellPosition)	Constructor with artifact, container and well position.
	PlacementsLink(Linkable<Placements> placements)	Constructor with placements object.
	PooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName, Linkable<Artifact> outputArtifact)	Constructor with input artifacts, pool name and output artifact.
	PoolsLink(Linkable<Pools> pools)	Constructor with pools object.
	ProgramStatusLink(Linkable<ProgramStatus> link)	Constructs a new ProgramStatusLink from a linkable program status.
	ReagentLotLink(Linkable<ReagentLot> link)	Constructs a new ReagentLotLink from a linkable reagent lot.
	ReagentLotsLink(Linkable<ReagentLots> link)	Creates a reagent lots link from a linkable object.
	ReagentsLink(Linkable<Reagents> link)	Creates a reagents link from a linkable object.
	SharedResultFile(Linkable<Artifact> link)	Creates a shared result file from a linkable artifact.
	StepConfiguration(Linkable<ProtocolStep> step)	Creates a step configuration from a linkable protocol step.
	StepCreation(Linkable<ProtocolStep> step)	Constructor taking a protocol step link.
	StepDetailsLink(Linkable<StepDetails> link)	Constructor taking a linkable object.
	StepSetupLink(Linkable<StepSetup> link)	Constructor taking a linkable object.
	Technician(Linkable<Researcher> technician)	Constructor taking a linkable researcher.
	UserLink(Linkable<Researcher> link)	Constructor taking a linkable researcher.

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

Modifier	Constructor	Description
	PooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName)	Constructor with input artifacts and pool name.
	PooledInputs(Collection<? extends Linkable<Artifact>> inputArtifacts, String poolName, Linkable<Artifact> outputArtifact)	Constructor with input artifacts, pool name and output artifact.

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)	Adds a permitted control type.
ReagentKitLink	ProtocolStep.addRequiredReagentKit(Linkable<ReagentKit> kit)	Adds a required reagent kit.
void	NextStep.setNextStep(Linkable<ProtocolStep> step)	Sets the next step from a linkable protocol step.
void	ProtocolStep.setProcessType(Linkable<ProcessType> processType)	Sets the process type for this step.

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

Modifier	Constructor	Description
	ControlTypeLink(Linkable<ControlType> link)	Constructor from a linkable control type.
	ProcessTypeLink(Linkable<ProcessType> link)	Constructor from a linkable process type.
	ReagentKitLink(Linkable<ReagentKit> link)	Constructor from a linkable reagent kit.

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)	Adds a protocol to this workflow.
StageLink	Workflow.addStage(Linkable<Stage> stage)	Adds a stage to this workflow.

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

Modifier	Constructor	Description
	ProtocolLink(Linkable<Protocol> link)	Constructor accepting a Linkable object.
	StageLink(Linkable<Stage> link)	Constructor accepting a Linkable object.
	WorkflowLink(Linkable<Workflow> link)	Constructor accepting a Linkable object.

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.
default SavedQuerySummary	ClarityAPI.runSavedQuery(Linkable<SavedQuery> query, OutputStream out)	Run a saved query and write the result to the given output stream.
SavedQuerySummary	ClarityAPI.runSavedQuery(Linkable<SavedQuery> query, OutputStream out, long maximumResults)	Run a saved query and write the result to the given output stream.

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

Modifier	Constructor	Description
	SavedQuerySummary(Linkable<SavedQuery> query, MediaType mediaType, long length)	Constructor.

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.
SavedQuerySummary	ClarityAPIImpl.runSavedQuery(Linkable<SavedQuery> query, OutputStream out, long maximumResults)	Run a saved query and write the result to the given output stream.
SavedQuerySummary	SavedQueryRunner.runSavedQuery(Linkable<SavedQuery> query, OutputStream out, long maximumResults)	Run a saved query and write the result to the given output stream.

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.