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Add getDefaultOrganism(), getOrganism(), and setOrganism() #19

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HenrikBengtsson opened this issue May 8, 2015 · 0 comments

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HenrikBengtsson commented May 8, 2015

Add getDefaultOrganism(), getOrganism(), and setOrganism(), where:

setOrganism() sets the organism field of the object, which by default is not set (=NULL).
getOrganism() gets the organism field. if not set, then falls back to returning getDefaultOrganism().
getDefaultOrganism() tries to infers the organism from the aroma-flavored directory structure, e.g. annotationData/organisms/<organism>/Ensembl/79/foo.fa => <organism>. If this fails, an exception is thrown.

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HenrikBengtsson added the enhancement label

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