[Bioperl-l] 0.7 aims; seqfeature interface

[Ewan Birney]

(I am seperating my posts for easier tracking my hilmar as suggested)

I think we should bring up a redesign possibly of the seqfeature
interface.

(a) having a location object

$seqfeature->location would return an object that was more like
a EMBL/GenBank location line but in objects. 

(this is for biocorba/fuzziness)

$seqfeature->start/end/strand will still be there and would
return extents of the location


    --- benefits - easier embl/genbank handling
                 - biocorba compatible
                 - can handle fuzziness in location 
                 - backwardly compatible with start/end/strand

    --- drawbacks - at least 1 other object per seqfeature 
                  - potentially start/end/strand could disagree with
                    location evidence in a naive implementation


(b) has_tag/each_tag_value/add_value 

-- better names for these subroutines? This is the correct
functionality...


(c) consistency of additional methods with
has_tag/each_tag_value/add_value methods


-- hilmar - do you have a view?


  


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