interface GeneAnnotationSource
Abstract interface for gene annotation sources
Enables dependent code to work with different sources of gene annotations, eg: Ensembl vs RefSeq
| Type Params | Return Type | Name and description |
|---|---|---|
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abstract java.util.Map<java.lang.String, java.lang.Integer> |
getCDS(IRegion region)Compute a map of gene symbols with the amount of coding sequence overlapped by each gene for the given region |
|
abstract Regions |
getExons(java.lang.String gene)
|
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abstract java.util.List<java.lang.String> |
getGenes(IRegion region)
|
Compute a map of gene symbols with the amount of coding sequence overlapped by each gene for the given region