Package ca.corefacility.bioinformatics.irida.model.assembly

Class GenomeAssemblyFromAnalysis

java.lang.Object

ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

All Implemented Interfaces:

IridaSequenceFile, IridaThing, Timestamped<java.lang.Long>, VersionedFileFields<java.lang.Long>

@Entity
public class GenomeAssemblyFromAnalysis
extends GenomeAssembly

Defines a genome assembly from an IRIDA-based analysis.

Constructor Summary

Constructors

Constructor	Description
GenomeAssemblyFromAnalysis(AnalysisSubmission assembly)

Method Summary

Modifier and Type	Method	Description
AnalysisSubmission	getAnalysisSubmission()
AnalysisOutputFile	getAssemblyOutput()	Get genome assembly AnalysisOutputFile.
java.nio.file.Path	getFile()	Gets the assembly file.
java.lang.Long	getFileRevisionNumber()	Get the version of the instance.
java.lang.String	getLabel()	Get a human readable label for this object.
void	incrementFileRevisionNumber()	Internally modify the file revision number to something new.
void	setAnalysisSubmission(AnalysisSubmission assembly)

Methods inherited from class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

addSampleGenomeAssemblyJoin, equals, getCreatedDate, getFileName, getFileSize, getFileSizeBytes, getId, hashCode, setId

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

add, add, getLink, getLinks, getRemoteStatus, getSelfHref, hasLink, hasLinks, removeLinks, setRemoteStatus, 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, setLabel

Constructor Detail

GenomeAssemblyFromAnalysis

public GenomeAssemblyFromAnalysis(AnalysisSubmission assembly)

Method Detail

getAnalysisSubmission

public AnalysisSubmission getAnalysisSubmission()

setAnalysisSubmission

public void setAnalysisSubmission(AnalysisSubmission assembly)

getAssemblyOutput

public AnalysisOutputFile getAssemblyOutput()

Get genome assembly AnalysisOutputFile.

Returns:

AnalysisOutputFile for a genome assembly AnalysisSubmission

getLabel

public java.lang.String getLabel()

Get a human readable label for this object.

Specified by:

getLabel in interface IridaThing

Overrides:

getLabel in class GenomeAssembly

Returns:

a human-readable label for the object.

getFile

public java.nio.file.Path getFile()

Gets the assembly file.

Specified by:

getFile in interface IridaSequenceFile

Specified by:

getFile in class GenomeAssembly

Returns:

The assembly file.

getFileRevisionNumber

public java.lang.Long getFileRevisionNumber()

Description copied from interface: VersionedFileFields

Get the version of the instance.

Returns:

the version of the instance.

incrementFileRevisionNumber

public void incrementFileRevisionNumber()

Description copied from interface: VersionedFileFields

Internally modify the file revision number to something new.