ubic.gemma.core.image.aba

Interface AllenBrainAtlasService

All Known Implementing Classes:

AllenBrainAtlasServiceImpl

public interface AllenBrainAtlasService

Author:

paul

Method Summary

Modifier and Type	Method and Description
AbaGene	getGene(Gene gene)
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.

Method Detail

getGene

AbaGene getGene(Gene gene)
         throws IOException

Parameters:

gene - gene to look up in ABA.

Returns:

AbaGene.

Throws:

IOException - if there is a problem while manipulating the file.

getGeneUrl

String getGeneUrl(Gene gene)

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

Parameters:

gene - gene

Returns:

an allen brain atlas gene details URL

getImagesFromImageSeries

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

Returns a collection of images from all the imageSeries given.

Parameters:

imageSeries - image series

Returns:

collection of images

getSagittalImageSeries

Collection<ImageSeries> getSagittalImageSeries(Gene gene)
                                        throws IOException

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.

Parameters:

gene - gene to look for

Returns:

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

Throws:

IOException - if there is a problem while manipulating the file