1.1 --- a/lib/alignment.py	Wed Nov 10 12:47:47 2010 +0300
     1.2 +++ b/lib/alignment.py	Wed Nov 17 21:02:10 2010 +0300
     1.3 @@ -19,16 +19,17 @@
     1.4      """ Alignment
     1.5      
     1.6      Mandatory data:
     1.7 -    *   sequences -- list of Sequence objects. Sequences don't contain gaps
     1.8 -         - see sequence.py module
     1.9      *   body -- dict 
    1.10          {<Sequence object>:[<Monomer object>,None,<Monomer object>]}
    1.11          keys are the Sequence objects, values are the lists, which
    1.12          contain monomers of those sequences or None for gaps in the
    1.13          corresponding sequence of
    1.14          alignment
    1.15 +    
    1.16 +    """
    1.17 +    # _sequences -- list of Sequence objects. Sequences don't contain gaps
    1.18 +    #  - see sequence.py module
    1.19  
    1.20 -    """
    1.21      def __init__(self, *args):
    1.22          """overloaded constructor
    1.23  
    1.24 @@ -48,15 +49,15 @@
    1.25          else:
    1.26              self.sequences, self.body = Alignment.from_fasta(args[0])
    1.27  
    1.28 -    def __len__(self):
    1.29 +    def length(self):
    1.30          """ Returns width, ie length of each sequence with gaps """
    1.31          return max([len(line) for line in self.body.values()])
    1.32  
    1.33 -    def thickness(self):
    1.34 +    def height(self):
    1.35          """ The number of sequences in alignment (it's thickness). """
    1.36          return len(self.body)
    1.37 -       
    1.38 -    def calc_identity(self):
    1.39 +
    1.40 +    def identity(self):
    1.41          """ Calculate the identity of alignment positions for colouring.
    1.42  
    1.43          For every (row, column) in alignment the percentage of the exactly