[Biojava-l] ResidueList & Annotatable

[Ann Loraine]

Hi,

My 2 cents on the discussion of the Sequence interface as a 
subinterface of ResidueList -

I also am worried about speed & memory - what happens when we 
try to build a ResidueList that represents a megabase-sized
sequence?  That's a lot of Residue Objects!

Perhaps the implementation can avoid creating these million +
Residues until someone calls the "residueAt(int it)" method -- sort of
a lazy evaluation strategy.  (Please forgive me if I misunderstand
the design.)

May I move on to another aspect of the data models at:

http://www.sanger.ac.uk/Users/td2/biojava_core_20000121/ ?

I have a question/comment about the Annotatable interface and its 
getAnnotation() method - which returns an Annotation Object.

Seems like it might be wise to have a getAnnotations()
(plural) method instead.  

For example, a Sequence could have many Annotations - gene
predictions, promoter elements, etc.

Or do you intend instead for each prediction, promoter element, etc be
represented by a different Sequence Object?  

-Ann

--
 Ann E. Loraine
 loraine@fruitfly.berkeley.edu
 http://www.fruitfly.org/~loraine

 Berkeley Drosophila Genome Project
 539 Life Science Addition
 U.C. Berkeley
 Berkeley, CA  94720
 TEL: 510-643-0657
 FAX: 510-643-9947