Issue 3687: DsLSRBioObjects issue                                                                                                                                                                                   (biomolecular-ftf)
Source:  (Mr. Philip Lijnzaad, p.lijnzaad@med.uu.nl)
Nature: Uncategorized Issue
Severity: 
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 {start,length}, 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
follows:

   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);
   }  

Resolution: split into issues 3870, 3871, 3872
Revised Text: 
Actions taken:
June 9, 2000: received issue
September 28, 2000: split into issues 3870, 3871, 3872
May 24, 2001: closed issue
Discussion: 

End of Annotations:=====
Date: Fri, 9 Jun 2000 15:39:29 +0100 (BST)
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From: Philip Lijnzaad <lijnzaad@ebi.ac.uk>
To: biomolecular-ftf@emerald.omg.org
cc: muilu@ebi.ac.uk
Subject: some issues ... 
Reply-to: lijnzaad@ebi.ac.uk
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Hi all,

my apologies with being so awfully late on this, a few days before OMG
Oslo
(where I will not be going, sorry).


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 {start,length}, 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
follows:

   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);
   }  

Date: Tue, 19 Sep 2000 12:39:34 +0100 (BST)
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From: Philip Lijnzaad <lijnzaad@ebi.ac.uk>
To: juergen@omg.org
cc: biomolecular-ftf@omg.org, senger@ebi.ac.uk, muilu@ebi.ac.uk
Subject: Issue 3687: split into new issues
Reply-to: lijnzaad@ebi.ac.uk
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Dear Juergen,

could you please, for the biomolecular-ftf, split issue 3687 into two
new
issues:

3687a: 

  typedef sequence<Interval> IntervalList; is missing from the spec;
  can this
  be added?

------------------------------------------------------------------------
3687b: 

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.

------------------------------------------------------------------------


                                                                      Philip
-- 
When C++ is your hammer, everything looks like a thumb. (Steven
Haflich)
-----------------------------------------------------------------------------
Philip Lijnzaad, lijnzaad@ebi.ac.uk \ European Bioinformatics
Institute,rm A2-24
+44 (0)1223 49 4639                 / Wellcome Trust Genome Campus,
Hinxton
+44 (0)1223 49 4468 (fax)           \ Cambridgeshire CB10 1SD,  GREAT
BRITAIN
PGP fingerprint: E1 03 BF 80 94 61 B6 FC  50 3D 1F 64 40 75 FB 53

Date: Tue, 19 Sep 2000 12:41:18 +0100 (BST)
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From: Philip Lijnzaad <lijnzaad@ebi.ac.uk>
To: biomolecular-ftf@omg.org
cc: senger@ebi.ac.uk, muilu@ebi.ac.uk
Subject: Issue 3687a (or whatever number): adding IntervalList
Reply-to: lijnzaad@ebi.ac.uk
Content-Type: text
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Dear all,


The EBI proposes as a resolution to 3687a (first sub-issue of 3687),
to add

  typedef sequence<Interval> IntervalList

to DsLSRBioObjects.idl

                                                                      Philip

-- 
When C++ is your hammer, everything looks like a thumb. (Steven
Haflich)
-----------------------------------------------------------------------------
Philip Lijnzaad, lijnzaad@ebi.ac.uk \ European Bioinformatics
Institute,rm A2-24
+44 (0)1223 49 4639                 / Wellcome Trust Genome Campus,
Hinxton
+44 (0)1223 49 4468 (fax)           \ Cambridgeshire CB10 1SD,  GREAT
BRITAIN
PGP fingerprint: E1 03 BF 80 94 61 B6 FC  50 3D 1F 64 40 75 FB 53