Bioperl: Start of alignment debate...

[Steve Chervitz]

Ewan,

Regarding this requirement:

4. The alignment should be able to be changed/manipulated 

  -- Removal/Addition of sequences 
  -- Truncated at the N or C terminii 
  -- The alignment internally changed 

Not all alignments need to be editable. Removing editability and using
factories to create new alignments would simplify the alignment object
itself. Having a class of immutable alignments would also ensure that
a given alignment hasn't been mangled, when this is important.

Steve Chervitz
sac@neomorphic.com

Ewan Birney writes:
 > 
 > I've started to lay out my ideas about sequence alignments
 > for bioperl at
 > 
 > http://bio.perl.org/Projects/SeqAlign/overview.html
 > 
 > at this moment it is just trying to gather together a list of
 > requirements about alignments. I am sure I have not got them all,
 > so if you have some use for alignments, please check the page
 > out and tell me what to add.
 > 
 > 
 > Ewan Birney
 > <birney@sanger.ac.uk>
 > http://www.sanger.ac.uk/Users/birney/
 > 
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