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

Class SequenceFilePair

java.lang.Object

ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

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

ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

All Implemented Interfaces:

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

@Entity
public class SequenceFilePair
extends SequencingObject

A pair of sequence files in forward/reverse orientation.

Nested Class Summary

Nested classes/interfaces inherited from class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

SequencingObject.ProcessingState

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String[]	forwardMatches
static java.lang.String[]	reverseMatches

Constructor Summary

Constructors

Constructor	Description
SequenceFilePair()
SequenceFilePair(SequenceFile file1, SequenceFile file2)

Method Summary

Modifier and Type	Method	Description
boolean	equals(java.lang.Object obj)
java.util.Set<SequenceFile>	getFiles()	Get the SequenceFiles associated with this SequencingObject
SequenceFile	getForwardSequenceFile()	Gets the forward SequenceFile from the pair.
java.lang.String	getLabel()	Get a human readable label for this object.
SequenceFile	getReverseSequenceFile()	Gets the reverse SequenceFile from the pair.
int	hashCode()
void	setFiles(java.util.Set<SequenceFile> files)	Set the SequenceFiles in this pair.
void	setModifiedDate(java.util.Date modifiedDate)	Set the modification time of this object
java.lang.String	toString()

Methods inherited from class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getAutomatedAssembly, getCreatedDate, getFileProcessor, getFileWithId, getId, getModifiedDate, getProcessingState, getQcEntries, getRemoteStatus, getSequencingRun, getSistrTyping, setAutomatedAssembly, setFileProcessor, setId, setProcessingState, setQcEntries, setRemoteStatus, setSequencingRun, setSistrTyping

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

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

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

Field Detail

forwardMatches

public static java.lang.String[] forwardMatches

reverseMatches

public static java.lang.String[] reverseMatches

Constructor Detail

SequenceFilePair

public SequenceFilePair()

SequenceFilePair

public SequenceFilePair(SequenceFile file1,
                        SequenceFile file2)

Method Detail

hashCode

public int hashCode()

Description copied from class: IridaRepresentationModel

Overrides:

hashCode in class SequencingObject

equals

public boolean equals(java.lang.Object obj)

Description copied from class: IridaRepresentationModel

Overrides:

equals in class SequencingObject

getForwardSequenceFile

public SequenceFile getForwardSequenceFile()

Gets the forward SequenceFile from the pair.

Returns:

The forward SequenceFile from the pair.

getReverseSequenceFile

public SequenceFile getReverseSequenceFile()

Gets the reverse SequenceFile from the pair.

Returns:

The reverse SequenceFile from the pair.

setModifiedDate

public void setModifiedDate(java.util.Date modifiedDate)

Description copied from interface: MutableIridaThing

Set the modification time of this object

Parameters:

modifiedDate - The date where this object was modified

getLabel

public java.lang.String getLabel()

Description copied from interface: IridaThing

Get a human readable label for this object.

Returns:

a human-readable label for the object.

toString

public java.lang.String toString()

Description copied from class: IridaRepresentationModel

Overrides:

toString in class IridaRepresentationModel

getFiles

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

Description copied from class: SequencingObject

Get the SequenceFiles associated with this SequencingObject

Specified by:

getFiles in class SequencingObject

Returns:

a Set of SequenceFile

setFiles

public void setFiles(java.util.Set<SequenceFile> files)

Set the SequenceFiles in this pair. Note it must contain 2 files.

Parameters:

files - The set of SequenceFiles