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.
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