AllenBrainAtlasService (Gemma 1.31.4 API)

All Known Implementing Classes:

AllenBrainAtlasServiceImpl
```
public interface AllenBrainAtlasService
```
Author:

paul

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	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