[Biojava-l] Re: introducing a location-less feature into BioJava

[hilmar.lapp@pharma.Novartis.com]

If, on the other hand, Feature would not contain a Location-property, i
could create a Feature object for the SET-domain (in general). A
distinct LocatedFeature object must then be constructed to link sequence
A to the SET-domain Feature, giving the location of the domain in
sequence A; and the same must be done for sequence B. But the so-created
distinct LocatedFeature objects would explicitly share (hold a reference
to) the same Feature object (for the SET-domain).

     Right. While the present design is similar to bioperl, it is contrary to
     how
     I guess most people design a sequence database with features (n-n).
     This makes it then possible to ask a database to return all sequences
     having a specific feature, and where this feature is. So, similarly
     you would like to be able to ask a specific Feature object for
     returning all its assignments to FeatureHolders, instead of having
     to iterate over all FeatureHolders and query each whether they contain
     a Feature of a particular type.

     The question is maybe whether or not FeatureHolders should own the
     Features they hold, in the sense that the location of the Feature
     refers to its holder. Or you look at Features as abstract types of
     their own, in the sense that they can be 'attached' to an arbitrary
     number of FeatureHolders, and each attachment has a location (and
     maybe even more properties, like a score, and the attachment to
     different strands does not necessarily make a different feature, so
     the strand may also be an attachment property).

          Hilmar