BSA 1.0 NO IDEA Avatar
  1. OMG Issue

BSA — DsLSRBioObjects issue

  • Key: BSA-18
  • Legacy Issue Number: 3687
  • Status: closed  
  • Source: ( Philip Lijnzaad)
  • Summary:

    We have been busy implementing the BSA spec, and there's a few things in the
    DsLSRBioObjects part that we would like your opinion on.

    The biggest one concerns the Alignment interface. As anticipated by all of us
    except Ewan, Alignment is tricky to implement efficiently because of
    gaps. The only way to do it is to repeatedly invoke get_seq_region, and
    seeing if you get back a null. Of course, an AlignmentEncoder can do this on
    the server-side, but it this is still clumsy (and optional).

    Our main proposal is to add an operation

    IntervalList get_gaps(in AlignmentElement element, in Interval the_interval);

    to the interface Alignment. It's job is to simply return all the gaps of a
    particular sequence in a particular alignment. For symmetry with
    get_seq_region(), the_interval is also given, thus limiting the gaps to those
    that you're interested in.

    [ Incidentally,

    typedef sequence<Interval> IntervalList;

    is missing from the spec; can this be added? ]

    One gap would be represented as


    , hence the use of Interval. We
    could add

    typedef Interval Gap;

    to make the semantics clearer (elsewhere, an Interval is an existing segment;
    here it denotes a missing segment). The coordinates of a gap would be those
    of the original sequence; gaps of length 0 are not allowed. A gap.start == 0
    would be before the first nucleotide/aminoacid; a gap.start = N is a gap
    between nucleotides/aminoacids N and N+1 (so gap.start = sequence.length
    would be after the last.

    Another proposal is to separate Alignment into more managable pieces as

    interface SimpleAlignment : CosLifeCycle::LifeCycleObject

    { // ... // here, everything get_seq_region() // ... }

    interface Alignment : SimpleAlignment

    { SeqRegion get_seq_region( in AlignmentElement element, in Interval the_interval) raises(ElementNotInAlignment, IntervalOutOfBounds); }

  • Reported: BSA 1.0b1 — Fri, 9 Jun 2000 04:00 GMT
  • Disposition: Resolved — BSA 1.0
  • Disposition Summary:

    split into issues 3870, 3871, 3872

  • Updated: Fri, 6 Mar 2015 20:57 GMT