[Biocorba-l] new idls available

[Juha Muilu]

Thanks for all for the good feedback and new ideas during the BOF meetings
here at the BOSC/ISMB!!! We made very nice progress!


I have compiled our talks into the IDLs, which are available here:

http://corba.ebi.ac.uk/~muilu/uml/bsane_tivoli/idl/bsane.idl
http://corba.ebi.ac.uk/~muilu/uml/bsane_tivoli/idl/seqcore.idl
http://corba.ebi.ac.uk/~muilu/uml/bsane_tivoli/idl/collection.idl
http://corba.ebi.ac.uk/~muilu/uml/bsane_tivoli/idl/comparison.idl

html-doc:
http://corba.ebi.ac.uk/~muilu/uml/bsane_tivoli/idl/bsane.html


Hope I have included all we were talking about. Please have a look and let
me know if something is missing/wrong.

We still should have time to have an another BOF if new ideas etc 
come up. I am happy to meet again.

Here are some comments and minor changes which came up while I was
writing the IDLs.

=1==============================================================
New interface AnnotatableSequence made:

    interface Annotatable  {
	AnnotationCollection get_annotations() ;
    };

    interface AnnotatableSequence : Annotatable { 
      SeqFeatureCollection get_seq_features();
    };

BioSequence inherits from this interface. 


=2=============================================================
SeqFeature interface inherits from Annotatable
to be able to add qualifying information.  

This can be slow, as were talking, because of number of those
entities can be high and we have many indirections :

SeqFeature.get_annotations() -> 
AnnotationCollection.get_annotations_by_name("key") ->
Annotation.get_value()


An improvement is to make inheritance directly from
AnnotationCollection or from a new simpler base class which has
just the methods needed:
 get_annotations_by_name   and perhaps
 get_annotations_as_name_value_pairs (convenience method.. if speed becomes an issue)

...We can also go back to original use of the plain name-value-pair
list (list of structs)



Same solution should be applied also to SearchHit and AlignmentElement
to be consistent. 
=3=============================================================

Alignment interface has now the method for getting the edited sequence
string instead of AnonymousSequence. Method is renamed:

string get_edited_sequence_string( in string key) 
 raises (IdentifierNotResolvable, DoesNotExist);

The gap-tokens can be resolved if original sequence has Alphabet. Original 
unmodified sequence can be found from the corresponding AlignmentElement 


Best Regards, Juha

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 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
 |European Bioinformatics Institute | Phone:  +44 (0)1223 494 624     |
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