[Bioperl-l] 0.7 aims; seqfeature interface

Ewan Birney birney@ebi.ac.uk
Mon, 13 Nov 2000 10:17:46 +0000 (GMT)

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

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

(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

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

-- hilmar - do you have a view?


Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420