[Biopython-dev] [Bug 1944] Align.Generic adding iterator and more

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1944


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
 Attachment #768 is|0                           |1
           obsolete|                            |




------- Comment #12 from biopython-bugzilla at maubp.freeserve.co.uk  2007-09-27 13:36 EST -------
Created an attachment (id=770)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=770&action=view)
Replacement Bio/Align/__init__.py (alignment update v5)

This implements a new alignment class which:
* directly subclasses the python list (as a list of SeqRecords)
* should be a fully backwards compatible with Bio.Align.Generic.Alignment
* implements __str__ and __repr__ methods which are useable on large alignment
* allows flexible subscripting using __getitem__
* enforces strict alphabet and length checking in __init__, append, extend,
__add__ and __radd__ (the last two give list like addition)

Provisos from comment 11 still apply.


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