Package ca.corefacility.bioinformatics.irida.service

Interface SequencingObjectService

All Superinterfaces:

CRUDService<java.lang.Long,SequencingObject>

All Known Implementing Classes:

SequencingObjectServiceImpl

public interface SequencingObjectService
extends CRUDService<java.lang.Long,SequencingObject>

Service for managing SequencingObjects and relationships with related objects

Method Summary

Modifier and Type	Method	Description
SampleSequencingObjectJoin	concatenateSequences(java.util.List<SequencingObject> toJoin, java.lang.String filename, Sample targetSample, boolean removeOriginals)	Concatenate a collection of SequencingObjects and save back to a Sample
SampleSequencingObjectJoin	createSequencingObjectInSample(SequencingObject seqObject, Sample sample)	Create a new SequencingObject associated with a Sample
java.util.Collection<SampleSequencingObjectJoin>	getSequencesForSampleOfType(Sample sample, java.lang.Class<? extends SequencingObject> type)	Get a collection of SampleSequencingObjectJoins assocaited with a given Sample and of the given class type
java.util.Set<SequencingObject>	getSequencingObjectsForAnalysisSubmission(AnalysisSubmission submission)	Get the set of SequencingObjects associated with a given AnalysisSubmission
java.util.Collection<SampleSequencingObjectJoin>	getSequencingObjectsForSample(Sample sample)	Get all the SequencingObjects associate with a given Sample
java.util.Set<SequencingObject>	getSequencingObjectsForSequencingRun(SequencingRun sequencingRun)	Get all the SequencingObjects associated with a given SequencingRun
<Type extends SequencingObject> java.util.Set<Type>	getSequencingObjectsOfTypeForAnalysisSubmission(AnalysisSubmission submission, java.lang.Class<Type> type)	Get all SequencingObjects of a given type associated with an AnalysisSubmission
<T extends SequencingObject> java.util.Map<Sample,T>	getUniqueSamplesForSequencingObjects(java.util.Set<T> sequenceFiles)	Gets a map of SequencingObjects and corresponding Sample s.
SequencingObject	readSequencingObjectForSample(Sample sample, java.lang.Long objectId)	Read a SequencingObject and verify that it belongs to a given Sample.
SequencingObject	updateRemoteStatus(java.lang.Long id, RemoteStatus remoteStatus)	Update the RemoteStatus for a SequencingObject

Methods inherited from interface ca.corefacility.bioinformatics.irida.service.CRUDService

count, create, delete, exists, findAll, findRevisions, findRevisions, list, list, list, read, readMultiple, search, search, update, updateFields, updateMultiple

Method Detail

createSequencingObjectInSample

SampleSequencingObjectJoin createSequencingObjectInSample(SequencingObject seqObject,
                                                          Sample sample)

Create a new SequencingObject associated with a Sample

Parameters:

seqObject - The SequencingObject to create

sample - the Sample to associate it with

Returns:

a new SampleSequencingObjectJoin describing the relationship

getSequencingObjectsForSample

java.util.Collection<SampleSequencingObjectJoin> getSequencingObjectsForSample(Sample sample)

Get all the SequencingObjects associate with a given Sample

Parameters:

sample - The Sample to get sequences for

Returns:

A collection of SampleSequencingObjectJoin

getSequencesForSampleOfType

java.util.Collection<SampleSequencingObjectJoin> getSequencesForSampleOfType(Sample sample,
                                                                             java.lang.Class<? extends SequencingObject> type)

Get a collection of SampleSequencingObjectJoins assocaited with a given Sample and of the given class type

Parameters:

sample - the Sample used in the join

type - The type of SequencingObject that must be in the join

Returns:

a Collection of SampleSequencingObjectJoin

readSequencingObjectForSample

SequencingObject readSequencingObjectForSample(Sample sample,
                                               java.lang.Long objectId)

Read a SequencingObject and verify that it belongs to a given Sample.

Parameters:

sample - the Sample to get the SequencingObject for

objectId - The SequencingObject ID

Returns:

A SequencingObject object

getUniqueSamplesForSequencingObjects

<T extends SequencingObject> java.util.Map<Sample,T> getUniqueSamplesForSequencingObjects(java.util.Set<T> sequenceFiles)
                                                                                         throws DuplicateSampleException

Gets a map of SequencingObjects and corresponding Sample s.

Type Parameters:

T - The type of sequencing object which should be returned

Parameters:

sequenceFiles - A Set of SequencingObjects.

Returns:

A Map of between Sample and SequencingObject.

Throws:

DuplicateSampleException - If there is a duplicate sample.

getSequencingObjectsForSequencingRun

java.util.Set<SequencingObject> getSequencingObjectsForSequencingRun(SequencingRun sequencingRun)

Get all the SequencingObjects associated with a given SequencingRun

Parameters:

sequencingRun - the run to get objects for

Returns:

a set of SequencingObject

updateRemoteStatus

SequencingObject updateRemoteStatus(java.lang.Long id,
                                    RemoteStatus remoteStatus)

Update the RemoteStatus for a SequencingObject

Parameters:

id - ID of the objet to update

remoteStatus - a RemoteStatus to set

Returns:

the updated SequencingObject

getSequencingObjectsForAnalysisSubmission

java.util.Set<SequencingObject> getSequencingObjectsForAnalysisSubmission(AnalysisSubmission submission)

Get the set of SequencingObjects associated with a given AnalysisSubmission

Parameters:

submission - the AnalysisSubmission

Returns:

the associated SequencingObjects

getSequencingObjectsOfTypeForAnalysisSubmission

<Type extends SequencingObject> java.util.Set<Type> getSequencingObjectsOfTypeForAnalysisSubmission(AnalysisSubmission submission,
                                                                                                    java.lang.Class<Type> type)

Get all SequencingObjects of a given type associated with an AnalysisSubmission

Type Parameters:

Type - a class type extending SequencingObject

Parameters:

submission - the AnalysisSubmission

type - the class type of SequencingObject to return

Returns:

a set of the requested type

concatenateSequences

SampleSequencingObjectJoin concatenateSequences(java.util.List<SequencingObject> toJoin,
                                                java.lang.String filename,
                                                Sample targetSample,
                                                boolean removeOriginals)
                                         throws ConcatenateException

Concatenate a collection of SequencingObjects and save back to a Sample

Parameters:

toJoin - the SequencingObjects to concatenate

filename - The name of the file to create on concatenation

targetSample - the Sample to save to

removeOriginals - Whether to remove the original SequencingObjects from the sample

Returns:

the new SampleSequencingObjectJoin

Throws:

ConcatenateException - if there was an error concatenating the sequences