[Biojava-l] FramedFeature interface

[Mark Schreiber]

Hi -

I agree with the comment that frame is sensitive to edits (and should be).
I actually wonder if a sequence that has features added to it should be
editable given that the edit might wreck some of the meaning in the
features.

Could I propose that features could listen for edit events and decide if
they should invalidate themselves if the edit is too major?

Mark

On Thu, 13 Sep 2001, Matthew Pocock wrote:

> Schreiber, Mark wrote:
> 
>  > Hi -
>  >
>  > Below is a work up for a possible FramedFeature interface
>  >
>  > Any comments?
> 
> 
> 
> Hi Mark,
> 
> This is my take on the issues. Don't let me stop you from writing code 
> and trying things out. After all, I rarely use frame information. I may 
> be missing the point somewhere along the line.
> 
> I'm fairly convinced that the strand and reading-frame of an exon are 
> orthogonal properties, and should not be co-encoded with something like 
> +/- [0..2]. My nose tells me that the reading frame is actualy a 
> propperty of the alignment between a transcript and a protein. This 
> property is then passed though several co-ordinate transforms to project 
> it down onto the genome, by which time it has become this hideous number 
> that is differently defined by almost every standard known to man. Of 
> course, we may be attempting to infer the protein, or the exact extent 
> of the exon which makes all of this more muddy than necisary. Classical 
> frames are very brital to simple edits like moving the start or end of 
> an exon. Three of the options I see are as follows:
> 
> 1) Frame can be added to it's own interface (re FramedFeature)
>    + we can just slot it in
>    - we will need a clear definition of how to interpret this frame
>    - it may not play well for multiple-inheritance with things like exon
> 
> 2) Frame can be added to the features that appear to need it e.g. Exon
>    + minimal change to APIs
>    - if Frame is applicable to several different types, we can't
>      easily re-use the frame concept
> 
> 3) Frame is moved into the HomologyFeature interface as an indication
>     of how the alignment between the different sequences (e.g. DNA vs
>     Protein) can be re-constructed.
>    + more robust to minor co-ordinate changes e.g. moving the start of
>      an exon
>    + appears to model the information more cleanly
>    + can be generalised to other features with intrinsic frames, not
>      necisarily in the range 0-2 e.g. micro-satelite repeats
>    - a break with tradition
>    - the API must be explained realy clearly
> 
> Does any of this tally with other peoples thoughts?
> 
> M
> 
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Mark Schreiber			Ph: 64 3 4797875
Rm 218				email mark_s@sanger.otago.ac.nz
Department of Biochemistry	email m.schreiber@clear.net.nz
University of Otago		
PO Box 56
Dunedin
New Zealand
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