[Biojava-dev] paired feature problem

[Keith James]

>>>>> "Doug" == Doug Rusch <drusch@tcag.org> writes:

    Doug> Is there a bug with the SimilarityPairBuilder in ssbind?  I
    Doug> am trying to instantiate the paired features, this is going
    Doug> fine, except that the sibling is coming back as null. Now I
    Doug> have been looking at how the templates are used to create
    Doug> these features. There is no way for the templates to know
    Doug> what their sibling feaure will be given that the sib hasnt
    Doug> been created yet much less assigned to the template.

You're right in all respects. Serves me right for not following my own
advice and including a test. I've added a setSibling method but
retained the sibling field in the template (for use in creating new
templates from an existing feature which has its sibling correctly
set) and fixed a less obvious defect in the features (I hadn't
overridden the superclass getTemplate). Updated the builder (will add
test after vacation).

There's a unit test for the feature too. Sorry for the inconvenience.

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -