1.1 --- a/lib/block.py	Fri May 21 20:30:40 2010 +0400
     1.2 +++ b/lib/block.py	Mon May 31 16:16:19 2010 +0400
     1.3 @@ -2,21 +2,18 @@
     1.4  
     1.5  import sys
     1.6  
     1.7 -import configure
     1.8  import project
     1.9  import sequence
    1.10  import monomer
    1.11 -import rooted_tree
    1.12 -from Lgamma import Lgamma
    1.13  
    1.14  class Block(object):
    1.15      """
    1.16      Mandatory data:
    1.17      *   self.project -- project object, which the block belongs to
    1.18 -    *   self.sequences - list of sequence objects, that contain monomers
    1.19 +    *   self.sequences - set of sequence objects that contain monomers
    1.20          and/or gaps, that constitute the block
    1.21 -    *   self.positions -- positions of the project.alignment that are
    1.22 -        included in the block
    1.23 +    *   self.positions -- list of positions of the project.alignment that
    1.24 +        are included in the block
    1.25  
    1.26      How to create a new block:
    1.27      >>> import project

     2.1 --- a/lib/project.py	Fri May 21 20:30:40 2010 +0400
     2.2 +++ b/lib/project.py	Mon May 31 16:16:19 2010 +0400
     2.3 @@ -7,7 +7,6 @@
     2.4  
     2.5  """
     2.6  
     2.7 -import configure
     2.8  import sequence
     2.9  import monomer
    2.10  

     3.1 --- a/lib/sequence.py	Fri May 21 20:30:40 2010 +0400
     3.2 +++ b/lib/sequence.py	Mon May 31 16:16:19 2010 +0400
     3.3 @@ -2,6 +2,12 @@
     3.4  import monomer 
     3.5  
     3.6  class Sequence(object):
     3.7 +    """
     3.8 +    Mandatory data:
     3.9 +    *   name -- str with the name of sequence
    3.10 +    *   description -- str with description of the sequence
    3.11 +    *   monomers -- list of monomer objects (aminoacids or nucleotides)
    3.12 +    """
    3.13      def __init__(self, name, description, monomers):
    3.14          self.name=name
    3.15          self.description=description