__init__ ( self,  alphabet )

Initialize a new Alignment object.

Arguments: o alphabet - The alphabet to use for the sequence objects that are created. This alphabet must be a gapped type.

add_sequence (
        self,
        descriptor,
        sequence,
        start=None,
        end=None,
        weight=1.0,
        )

Add a sequence to the alignment.

This doesn't do any kind of alignment, it just adds in the sequence object, which is assumed to be prealigned with the existing sequences.

Arguments: o descriptor - The descriptive id of the sequence being added. o sequence - A string with sequence info. o start - You can explicitly set the start point of the sequence. This is useful (at least) for BLAST alignments, which can just be partial alignments of sequences. o end - Specify the end of the sequence, which is important for the same reason as the start. o weight - The weight to place on the sequence in the alignment. By default, all sequences have the same weight. (0.0 => no weight, 1.0 => highest weight)

get_alignment_length ( self )

Return the maximum length of the alignment.

All objects in the alignment should (hopefully) have the same length. This function will go through and find this length by finding the maximum length of sequences in the alignment.

get_all_seqs ( self )

Return all of the sequences involved in the alignment.

The return value is a list of SeqRecord objects.

get_column ( self,  col )

Returns a string containing a given column

get_seq_by_num ( self,  number )

Retrieve a sequence by the number of the sequence in the consensus.

Returns: o A Seq object for the requested sequence.

Raises: o IndexError - If the specified number is out of range.