[Seqan-dev] Align Module Changes

[Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>]

Dear all,

I have just committed a major update to the align module in revision 
124XXX. It will take a few minutes until the API documentation at 
docs.seqan.de is up to date and we still have to adapt the alignment 
tutorial.

This commit makes large changes (to the better!) to the alignment API 
and also includes updates to all SeqAn library and application code 
(excluding SnpStore, for which I will write another email later).

The mainly visible change is that the interface to the the 
globalAlignment(), localAlignment() and Waterman-Eggert declumping 
algorithms change. Please see the API documentation and updated tutorial 
for the new interface:

  http://docs.seqan.de/
  http://trac.seqan.de/wiki/Tutorial/Alignments

Other major changes include:

* Major update to the Array Gaps class to provide a more intuitive 
interface for clipping alignments.

* Better API documentation of the whole module.

* A clearer structure of the module.

* The Anchor Gaps class now lives in the module align and not in the 
module store.

* The module graph_align is merged into the module align

If you have any problems with porting your old code over, do not 
hesitate to send an email to the mailing list and ask for help!

Kind regards, in the name of the SeqAn team,
Manuel Holtgrewe