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

Class GenomeAssembly

java.lang.Object

ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

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

All Implemented Interfaces:

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

Direct Known Subclasses:

GenomeAssemblyFromAnalysis, UploadedAssembly

@Entity
public abstract class GenomeAssembly
extends IridaRepresentationModel
implements IridaThing, IridaSequenceFile, VersionedFileFields<java.lang.Long>

Defines a genome assembly which can be associated with a sample.

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	GenomeAssembly()
	GenomeAssembly(java.util.Date createdDate)

Method Summary

Modifier and Type	Method	Description
void	addSampleGenomeAssemblyJoin(SampleGenomeAssemblyJoin join)	Add a sample to this assembly
boolean	equals(java.lang.Object obj)
java.util.Date	getCreatedDate()	Get the created date of the object
abstract java.nio.file.Path	getFile()	Gets the assembly file.
java.lang.String	getFileName()	The base name of the file
java.lang.String	getFileSize()	Get human-readable file size.
long	getFileSizeBytes()	Get the size of the genome assembly files
java.lang.Long	getId()	Get the numerical identifier for this object
java.lang.String	getLabel()	Get a human readable label for this object.
int	hashCode()
void	setId(java.lang.Long id)

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

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

getFileRevisionNumber, incrementFileRevisionNumber

Constructor Detail

GenomeAssembly

protected GenomeAssembly()

GenomeAssembly

public GenomeAssembly(java.util.Date createdDate)

Method Detail

getLabel

public java.lang.String getLabel()

Description copied from interface: IridaThing

Get a human readable label for this object.

Specified by:

getLabel in interface IridaThing

Returns:

a human-readable label for the object.

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

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

getFileSizeBytes

public long getFileSizeBytes()
                      throws java.io.IOException

Get the size of the genome assembly files

Returns:

file size

Throws:

java.io.IOException - if the file cannot be read

addSampleGenomeAssemblyJoin

public void addSampleGenomeAssemblyJoin(SampleGenomeAssemblyJoin join)

Add a sample to this assembly

Parameters:

join - the SampleGenomeAssemblyJoin to add

getFileSize

public java.lang.String getFileSize()

Get human-readable file size.

Specified by:

getFileSize in interface IridaSequenceFile

Returns:

A human-readable file size.

getFile

public abstract java.nio.file.Path getFile()

Gets the assembly file.

Specified by:

getFile in interface IridaSequenceFile

Returns:

The assembly file.

getFileName

public java.lang.String getFileName()

Description copied from interface: IridaSequenceFile

The base name of the file

Specified by:

getFileName in interface IridaSequenceFile

Returns:

a string base name of the file

hashCode

public int hashCode()

Description copied from class: IridaRepresentationModel

Overrides:

hashCode in class IridaRepresentationModel

setId

public void setId(java.lang.Long id)

equals

public boolean equals(java.lang.Object obj)

Description copied from class: IridaRepresentationModel

Overrides:

equals in class IridaRepresentationModel