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

Class SequenceFile

java.lang.Object

ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

All Implemented Interfaces:

IridaSequenceFile, IridaThing, MutableIridaThing, RemoteSynchronizable, Timestamped<java.lang.Long>, VersionedFileFields<java.lang.Long>, java.lang.Comparable<SequenceFile>

@Entity
public class SequenceFile
extends IridaRepresentationModel
implements MutableIridaThing, java.lang.Comparable<SequenceFile>, VersionedFileFields<java.lang.Long>, IridaSequenceFile, RemoteSynchronizable

A file that may be stored somewhere on the file system and belongs to a particular Sample.

Constructor Summary

Constructors

Constructor	Description
SequenceFile()
SequenceFile(java.nio.file.Path sampleFile)	Create a new SequenceFile with the given file Path

Method Summary

Modifier and Type	Method	Description
void	addOptionalProperty(java.lang.String key, java.lang.String value)	Add one optional property to the map of properties
int	compareTo(SequenceFile other)
boolean	equals(java.lang.Object other)
java.util.Date	getCreatedDate()	Get the created date of the object
AnalysisFastQC	getFastQCAnalysis()
java.nio.file.Path	getFile()	Get the location on the file system where the sequence file is stored
java.lang.String	getFileName()	The base name of the file
java.lang.Long	getFileRevisionNumber()	Get the version of the instance.
java.lang.String	getFileSize()	Get the size of the file.
java.lang.Long	getId()	Get the numerical identifier for this object
java.lang.String	getLabel()	Get a human readable label for this object.
java.util.Date	getModifiedDate()	Get the date that this object was last modified
java.util.Map<java.lang.String,java.lang.String>	getOptionalProperties()	Get the Map of optional properties
java.lang.String	getOptionalProperty(java.lang.String key)	Get an individual optional property
RemoteStatus	getRemoteStatus()	Get the RemoteStatus for this object if it was read from a remote source
java.lang.String	getUploadSha256()	Get the sha256 checksum for a file when it was uploaded.
int	hashCode()
void	incrementFileRevisionNumber()	Internally modify the file revision number to something new.
void	setFastQCAnalysis(AnalysisFastQC fastqcAnalysis)	Set the AnalysisFastQC for this SequenceFile.
void	setFile(java.nio.file.Path file)
void	setId(java.lang.Long id)	Set the numerical identifier for this object
void	setModifiedDate(java.util.Date modifiedDate)	Set the modification time of this object
void	setOptionalProperties(java.util.Map<java.lang.String,java.lang.String> optionalProperties)	Set the Map of optional properties
void	setRemoteStatus(RemoteStatus remoteStatus)	Set the RemoteStatus for this object if it was read from a remote source
void	setUploadSha256(java.lang.String uploadSha256)

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, setLabel

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

isRemote

Constructor Detail

SequenceFile

public SequenceFile()

SequenceFile

public SequenceFile(java.nio.file.Path sampleFile)

Create a new SequenceFile with the given file Path

Parameters:

sampleFile - The Path to a SequenceFile

Method Detail

equals

public boolean equals(java.lang.Object other)

Description copied from class: IridaRepresentationModel

Overrides:

equals in class IridaRepresentationModel

hashCode

public int hashCode()

Description copied from class: IridaRepresentationModel

Overrides:

hashCode in class IridaRepresentationModel

compareTo

public int compareTo(SequenceFile other)

Specified by:

compareTo in interface java.lang.Comparable<SequenceFile>

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

getFile

public java.nio.file.Path getFile()

Description copied from interface: IridaSequenceFile

Get the location on the file system where the sequence file is stored

Specified by:

getFile in interface IridaSequenceFile

Returns:

the physical location of the file.

setFile

public void setFile(java.nio.file.Path file)

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

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

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

setModifiedDate

public void setModifiedDate(java.util.Date modifiedDate)

Description copied from interface: MutableIridaThing

Set the modification time of this object

Specified by:

setModifiedDate in interface MutableIridaThing

Parameters:

modifiedDate - The date where this object was modified

getFileRevisionNumber

public java.lang.Long getFileRevisionNumber()

Description copied from interface: VersionedFileFields

Get the version of the instance.

Specified by:

getFileRevisionNumber in interface VersionedFileFields<java.lang.Long>

Returns:

the version of the instance.

addOptionalProperty

public void addOptionalProperty(java.lang.String key,
                                java.lang.String value)

Add one optional property to the map of properties

Parameters:

key - The key of the property to add

value - The value of the property to add

getOptionalProperties

public java.util.Map<java.lang.String,java.lang.String> getOptionalProperties()

Get the Map of optional properties

Returns:

A Map<String,String> of all the optional propertie

getOptionalProperty

public java.lang.String getOptionalProperty(java.lang.String key)

Get an individual optional property

Parameters:

key - The key of the property to read

Returns:

A String of the property's value

getFileSize

public java.lang.String getFileSize()

Get the size of the file.

Specified by:

getFileSize in interface IridaSequenceFile

Returns:

The String representation of the file size

setOptionalProperties

public void setOptionalProperties(java.util.Map<java.lang.String,java.lang.String> optionalProperties)

Set the Map of optional properties

Parameters:

optionalProperties - A Map<String,String> of all the optional properties for this object

incrementFileRevisionNumber

public void incrementFileRevisionNumber()

Description copied from interface: VersionedFileFields

Internally modify the file revision number to something new.

Specified by:

incrementFileRevisionNumber in interface VersionedFileFields<java.lang.Long>

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

getFastQCAnalysis

public AnalysisFastQC getFastQCAnalysis()

setFastQCAnalysis

public void setFastQCAnalysis(AnalysisFastQC fastqcAnalysis)
                       throws AnalysisAlreadySetException

Set the AnalysisFastQC for this SequenceFile.

Parameters:

fastqcAnalysis - the analysis to set.

Throws:

AnalysisAlreadySetException - if the analysis has already been set for this SequenceFile.

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

getUploadSha256

public java.lang.String getUploadSha256()

Get the sha256 checksum for a file when it was uploaded. NOTE: This checksum may not be the same as the sha256 for the current file. The checksum from the originally uploaded file is saved so an uploader can verify its file upload.

Returns:

the string sha256 for the uploaded file.

setUploadSha256

public void setUploadSha256(java.lang.String uploadSha256)