[basedb-devel] setting annotation values programmatically

[Micha Bayer]

Hi all,

I am in the final throes of adding the custom interface to the tab2mage
importer plugin but I have one more thing to do before it all works as
specified, and that is to set values for the experimental factors on
each of the raw bioassays added to the experiment so they can all be
displayed in the experiment's detail view (at the moment I am just
getting an empty list). 

I have been looking through the API and the dev docu for this but to no
avail. Can anyone point me in the right direction here? 

I think the raw bioassays should probably be inheriting these values
from the Sample objects they are linked to but I figure out how to a)
add an annotation to a sample or any other item for that matter, and b)
how to let the bioassay inherit this programmatically.

Cheers

Micha

==
Dr Micha M Bayer
Bioinformatics Specialist
Genetics Programme
The Scottish Crop Research Institute
Invergowrie
Dundee
DD2 5DA
Scotland, UK
Telephone +44(0)1382 562731 ext. 2309
Fax +44(0)1382 562426
http://www.scri.ac.uk/staff/michabayer
==
 

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Re: [basedb-devel] setting annotation values programmatically

[Nicklas Nordborg]

Micha Bayer wrote:
 Hi all,
 
 I am in the final throes of adding the custom interface to the tab2mage
 importer plugin but I have one more thing to do before it all works as
 specified, and that is to set values for the experimental factors on
 each of the raw bioassays added to the experiment so they can all be
 displayed in the experiment's detail view (at the moment I am just
 getting an empty list). 
 
 I have been looking through the API and the dev docu for this but to no
 avail. Can anyone point me in the right direction here? 
 
 I think the raw bioassays should probably be inheriting these values
 from the Sample objects they are linked to but I figure out how to a)
  add an annotation to a sample or any other item

Annotatable item = ...
AnnotationType at = ...
Annotation a = item.getAnnotationSet().getAnnotation(at);

// For a single annotation value
a.setValue(...);

// if it is multiple values
a.setValues(...);

 b) how to let the bioassay inherit this programmatically.

Annotatable child = ...
Annotatable parent = ...
AnnotationType at = ...
Annotation a = parent.getAnnotationSet().getAnnotation(at);

// To inherit a single annotation
child.getAnnotationSet().inheritAnnotation(a);

// To inherit all annotations
child.getAnnotationSet().inheritAnnotationSet(parent.getAnnotationSet());

/Nicklas

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