alignment.positions — list of residue-residue alignment positions (including gaps)

This is a list of all 'positions' in the alignment. Unlike individual sequences in the alignment (see Section 6.17), which are lists of the residues in those sequences (not including gaps) the 'positions' correspond to columns in the alignment file, including gaps. Each element in the list contains a method get_residue(seq) which, given a sequence in the same alignment, returns the residue in that sequence which is aligned at that position, or None if a gap is present.

Note that chain breaks are considered to have zero width, and thus fall 'between' alignment positions; they do not count as alignment positions.