1.1 --- a/allpy/base.py	Thu Dec 16 19:24:22 2010 +0300
     1.2 +++ b/allpy/base.py	Thu Dec 16 20:42:42 2010 +0300
     1.3 @@ -336,43 +336,43 @@
     1.4      """
     1.5      pass
     1.6  
     1.7 -    ## Unclean code follows
     1.8 +class Block(object):
     1.9 +    """Block of alignment.
    1.10  
    1.11 -class Block(object):
    1.12 -    """ Block of alignment
    1.13 -
    1.14 -    Mandatory data:
    1.15 -
    1.16 -    *   self.alignment -- alignment object, which the block belongs to
    1.17 -    *   self.sequences - set of sequence objects that contain monomers
    1.18 -        and/or gaps, that constitute the block
    1.19 -    *   self.positions -- list of positions of the alignment.body that
    1.20 -        are included in the block; position[i+1] is always to the right from position[i]
    1.21 -
    1.22 -    Don't change self.sequences -- it may be a link to other block.sequences
    1.23 -
    1.24 -    How to create a new block:
    1.25 -
    1.26 -    >>> import alignment
    1.27 -    >>> import block
    1.28 -    >>> proj = alignment.Alignment(open("test.fasta"))
    1.29 -    >>> block1 = block.Block(proj)
    1.30 +    Block is intersection of a set of columns & a set of rows. Most of blocks
    1.31 +    look like rectangular part of alignment if you shuffle alignment rows the
    1.32 +    right way.
    1.33      """
    1.34  
    1.35 -    def __init__(self, alignment, sequences=None, positions=None):
    1.36 -        """ Builds new block from alignment
    1.37 +    alignment = None
    1.38 +    """Alignment the block belongs to."""
    1.39  
    1.40 -        if sequences==None, all sequences are used
    1.41 -        if positions==None, all positions are used
    1.42 +    sequences = ()
    1.43 +    """List of sequences in block."""
    1.44 +
    1.45 +    columns = ()
    1.46 +    """List of columns in block."""
    1.47 +
    1.48 +    def __init__(self, alignment, sequences=None, columns=None):
    1.49 +        """Build new block from alignment.
    1.50 +
    1.51 +        If sequences are not given, the block uses all sequences in alignment.
    1.52 +
    1.53 +        If columns are not given, the block uses all columns in alignment.
    1.54 +
    1.55 +        In both cases we use exactly the list used in alignment, thus, if new
    1.56 +        sequences or columns are added to alignment, the block tracks this too.
    1.57          """
    1.58 -        if sequences == None:
    1.59 -            sequences = set(alignment.sequences) # copy
    1.60 -        if positions == None:
    1.61 -            positions = range(len(alignment))
    1.62 +        if sequences is None:
    1.63 +            sequences = alignment.sequences
    1.64 +        if colums is None:
    1.65 +            columns = alignment.columns
    1.66          self.alignment = alignment
    1.67          self.sequences = sequences
    1.68          self.positions = positions
    1.69  
    1.70 +    ## Unclean code follows
    1.71 +
    1.72      def save_fasta(self, out_file, long_line=70, gap='-'):
    1.73          """ Saves alignment to given file in fasta-format
    1.74