[Biojava-l] Complement feature in CDS table

[Thomas Down]

Once upon a time, Y D Sun wrote:
> > 
> > The complement(xxx..yyy) stuff is the feature's location, 
> > rather than part of the qualifier-value data.  In BioJava, 
> > this will be represented by a feature having a location from 
> > xxx to yyy, and being on the negative strand.
> > 
> 
> I want to check if a CDS contains the keyword "complement". Is there any
> method to do so?

If the EMBL entry really uses complement as a keyword (i.e.
it contains a /complement= qualifier) then I guess you've
found a bug in BioJava -- please could you send me the EMBL
file you're working with.

However, if you've just got entries which look like:

  FT   misc_feature    complement(57216..57545)
  FT                   /note="match: STS: Em:HSB298YH5 Em:Z53425"

In this case, the "complement" just means that the feature is
located in the reverse orientation.  If you load it into BioJava,
you will find this feature table record represented by a StrandedFeature
with the strand property set to NEGATIVE

    Thomas.