Package ca.corefacility.bioinformatics.irida.service

Interface GenomeAssemblyService

All Superinterfaces:

CRUDService<java.lang.Long,GenomeAssembly>

All Known Implementing Classes:

GenomeAssemblyServiceImpl

public interface GenomeAssemblyService
extends CRUDService<java.lang.Long,GenomeAssembly>

A service for storing and retrieving GenomeAssembly entities.

Method Summary

Modifier and Type	Method	Description
SampleGenomeAssemblyJoin	createAssemblyInSample(Sample sample, GenomeAssembly assembly)	Create a new GenomeAssembly in the given Sample
java.util.Collection<SampleGenomeAssemblyJoin>	getAssembliesForSample(Sample sample)	Get all GenomeAssembly for the given Sample
GenomeAssembly	getGenomeAssemblyForSample(Sample sample, java.lang.Long genomeAssemblyId)	Gets the genome assembly for a sample.
void	removeGenomeAssemblyFromSample(Sample sample, java.lang.Long genomeAssemblyId)	Deletes the given genome assembly from the given sample.

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

createAssemblyInSample

SampleGenomeAssemblyJoin createAssemblyInSample(Sample sample,
                                                GenomeAssembly assembly)

Create a new GenomeAssembly in the given Sample

Parameters:

sample - the sample to add a new assembly

assembly - the assembly to create

Returns:

a new SampleGenomeAssemblyJoin

getAssembliesForSample

java.util.Collection<SampleGenomeAssemblyJoin> getAssembliesForSample(Sample sample)

Get all GenomeAssembly for the given Sample

Parameters:

sample - the sample to get assemblies for

Returns:

a collection of SampleGenomeAssemblyJoin

getGenomeAssemblyForSample

GenomeAssembly getGenomeAssemblyForSample(Sample sample,
                                          java.lang.Long genomeAssemblyId)

Gets the genome assembly for a sample.

Parameters:

sample - The sample.

genomeAssemblyId - The id of the genome assembly.

Returns:

The GenomeAssembly with the given information.

removeGenomeAssemblyFromSample

void removeGenomeAssemblyFromSample(Sample sample,
                                    java.lang.Long genomeAssemblyId)

Deletes the given genome assembly from the given sample.

Parameters:

sample - The sample.

genomeAssemblyId - The genome assembly.