Package ubic.gemma.core.image.aba

Class AllenBrainAtlasServiceImpl

java.lang.Object

ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl

All Implemented Interfaces:

AllenBrainAtlasService

@Component
public class AllenBrainAtlasServiceImpl
extends Object
implements AllenBrainAtlasService

Acts as a convenient front end to the Allen Brain Atlas REST (web) services Used the ABAApi.java as the original template for this Service (found in ABA demo code). For the most current API regarding these methods go to brain map DATA API web page NO AJAX Methods directly exposed by this service.

Author:

kelsey

Constructor Summary

Constructors

Constructor	Description
AllenBrainAtlasServiceImpl(Path appDataHome)

Method Summary

Modifier and Type	Method	Description
AbaGene	getGene(Gene gene)	Given a gene too look for for will return the corresponding abaGene (useful for finding images)
String	getGeneUrl(Gene gene)	Given a Gemma gene object returns an allen brain atlas gene URL
Collection<Image>	getImagesFromImageSeries(Collection<ImageSeries> imageSeries)	Returns a collection of images from all the imageSeries given.
Collection<ImageSeries>	getSagittalImageSeries(Gene gene)	Given a Gene, returns all the image series that contain sagittal images for the given gene.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AllenBrainAtlasServiceImpl

@Autowired
public AllenBrainAtlasServiceImpl(@Value("gemma.appdata.home")
                                  Path appDataHome)

Method Detail

getGene

public AbaGene getGene(Gene gene)

Given a gene too look for for will return the corresponding abaGene (useful for finding images)

Specified by:

getGene in interface AllenBrainAtlasService

Parameters:

gene - the gene to look for in ABA.

Returns:

ABA gene

Throws:

IllegalArgumentException - when the given gene does not have an NCBI ID.

getGeneUrl

public String getGeneUrl(Gene gene)

Description copied from interface: AllenBrainAtlasService

Given a Gemma gene object returns an allen brain atlas gene URL

Specified by:

getGeneUrl in interface AllenBrainAtlasService

Parameters:

gene - gene

Returns:

an allen brain atlas gene details URL

getImagesFromImageSeries

public Collection<Image> getImagesFromImageSeries(Collection<ImageSeries> imageSeries)

Description copied from interface: AllenBrainAtlasService

Returns a collection of images from all the imageSeries given.

Specified by:

getImagesFromImageSeries in interface AllenBrainAtlasService

Parameters:

imageSeries - image series

Returns:

collection of images

getSagittalImageSeries

public Collection<ImageSeries> getSagittalImageSeries(Gene gene)

Description copied from interface: AllenBrainAtlasService

Given a Gene, returns all the image series that contain sagittal images for the given gene. Each series will only contain one image from the middle of the series.

Specified by:

getSagittalImageSeries in interface AllenBrainAtlasService

Parameters:

gene - gene to look for

Returns:

all the image series that contain sagittal images for the given gene