Package ca.corefacility.bioinformatics.irida.model.sequenceFile

Class SequencingObject

java.lang.Object

ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

All Implemented Interfaces:

IridaThing, MutableIridaThing, RemoteSynchronizable, Timestamped<java.lang.Long>

Direct Known Subclasses:

Fast5Object, SequenceFilePair, SingleEndSequenceFile

@Entity
public abstract class SequencingObject
extends IridaRepresentationModel
implements MutableIridaThing, RemoteSynchronizable

Objects that were obtained from some sequencing platform.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SequencingObject.ProcessingState	The status of the file processing upon upload

Constructor Summary

Constructors

Constructor	Description
SequencingObject()

Method Summary

Modifier and Type	Method	Description
boolean	equals(java.lang.Object obj)
AnalysisSubmission	getAutomatedAssembly()
java.util.Date	getCreatedDate()	Get the created date of the object
java.lang.String	getFileProcessor()
abstract java.util.Set<SequenceFile>	getFiles()	Get the SequenceFiles associated with this SequencingObject
SequenceFile	getFileWithId(java.lang.Long id)	Get the SequenceFile with the given id in this object's files collection
java.lang.Long	getId()	Get the numerical identifier for this object
java.util.Date	getModifiedDate()	Get the date that this object was last modified
SequencingObject.ProcessingState	getProcessingState()
java.util.Set<QCEntry>	getQcEntries()
RemoteStatus	getRemoteStatus()	Get the RemoteStatus for this object if it was read from a remote source
SequencingRun	getSequencingRun()
AnalysisSubmission	getSistrTyping()
int	hashCode()
void	setAutomatedAssembly(AnalysisSubmission automatedAssembly)
void	setFileProcessor(java.lang.String fileProcessor)
void	setId(java.lang.Long id)	Set the numerical identifier for this object
void	setProcessingState(SequencingObject.ProcessingState processingState)
void	setQcEntries(java.util.Set<QCEntry> qcEntries)
void	setRemoteStatus(RemoteStatus remoteStatus)	Set the RemoteStatus for this object if it was read from a remote source
void	setSequencingRun(SequencingRun sequencingRun)
void	setSistrTyping(AnalysisSubmission sistrTyping)

Methods inherited from class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

add, add, getLink, getLinks, getSelfHref, hasLink, hasLinks, removeLinks, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ca.corefacility.bioinformatics.irida.model.IridaThing

getIdentifier, getLabel, setLabel

Methods inherited from interface ca.corefacility.bioinformatics.irida.model.MutableIridaThing

setModifiedDate

Methods inherited from interface ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable

isRemote

Constructor Detail

SequencingObject

public SequencingObject()

Method Detail

getId

public java.lang.Long getId()

Description copied from interface: IridaThing

Get the numerical identifier for this object

Specified by:

getId in interface IridaThing

Specified by:

getId in interface Timestamped<java.lang.Long>

Returns:

the numerical identifier for the object

setId

public void setId(java.lang.Long id)

Description copied from interface: MutableIridaThing

Set the numerical identifier for this object

Specified by:

setId in interface MutableIridaThing

Parameters:

id - The ID to set

getCreatedDate

public java.util.Date getCreatedDate()

Description copied from interface: Timestamped

Get the created date of the object

Specified by:

getCreatedDate in interface Timestamped<java.lang.Long>

Returns:

A Date object of the created date

getModifiedDate

public java.util.Date getModifiedDate()

Description copied from interface: MutableIridaThing

Get the date that this object was last modified

Specified by:

getModifiedDate in interface MutableIridaThing

Returns:

Date object of the modified date

getSequencingRun

public SequencingRun getSequencingRun()

setSequencingRun

public void setSequencingRun(SequencingRun sequencingRun)

getFiles

public abstract java.util.Set<SequenceFile> getFiles()

Get the SequenceFiles associated with this SequencingObject

Returns:

a Set of SequenceFile

getFileWithId

public SequenceFile getFileWithId(java.lang.Long id)

Get the SequenceFile with the given id in this object's files collection

Parameters:

id - the ID of the SequenceFile to get

Returns:

a SequenceFile

equals

public boolean equals(java.lang.Object obj)

Description copied from class: IridaRepresentationModel

Overrides:

equals in class IridaRepresentationModel

hashCode

public int hashCode()

Description copied from class: IridaRepresentationModel

Overrides:

hashCode in class IridaRepresentationModel

getAutomatedAssembly

public AnalysisSubmission getAutomatedAssembly()

setAutomatedAssembly

public void setAutomatedAssembly(AnalysisSubmission automatedAssembly)

getSistrTyping

public AnalysisSubmission getSistrTyping()

setSistrTyping

public void setSistrTyping(AnalysisSubmission sistrTyping)

getRemoteStatus

public RemoteStatus getRemoteStatus()

Description copied from class: IridaRepresentationModel

Get the RemoteStatus for this object if it was read from a remote source

Specified by:

getRemoteStatus in interface RemoteSynchronizable

Overrides:

getRemoteStatus in class IridaRepresentationModel

Returns:

a RemoteStatus

setRemoteStatus

public void setRemoteStatus(RemoteStatus remoteStatus)

Description copied from class: IridaRepresentationModel

Set the RemoteStatus for this object if it was read from a remote source

Specified by:

setRemoteStatus in interface RemoteSynchronizable

Overrides:

setRemoteStatus in class IridaRepresentationModel

Parameters:

remoteStatus - the RemoteStatus object

getQcEntries

public java.util.Set<QCEntry> getQcEntries()

setQcEntries

public void setQcEntries(java.util.Set<QCEntry> qcEntries)

setProcessingState

public void setProcessingState(SequencingObject.ProcessingState processingState)

getProcessingState

public SequencingObject.ProcessingState getProcessingState()

setFileProcessor

public void setFileProcessor(java.lang.String fileProcessor)

getFileProcessor

public java.lang.String getFileProcessor()