1.1 --- a/allpy/base.py	Fri Jul 08 16:20:20 2011 +0400
     1.2 +++ b/allpy/base.py	Fri Jul 08 18:30:04 2011 +0400
     1.3 @@ -446,25 +446,10 @@
     1.4      types = base
     1.5      """Mapping of related types. SHOULD be redefined in subclasses."""
     1.6  
     1.7 -    def __init__(self, alignment):
     1.8 -        self.alignment = alignment
     1.9 -        super(Column, self).__init__()
    1.10 -
    1.11      def __hash__(self):
    1.12          """Return hash by identity."""
    1.13          return id(self)
    1.14  
    1.15 -    def MyIndex(self):
    1.16 -        for index, column in enumerate(self.alignment.columns):
    1.17 -            if column is self: return index
    1.18 -        raise ValueException
    1.19 -
    1.20 -    def __repr__(self):
    1.21 -    #!!!!!!!!! READ HOW index OF LIST COMPARES OBJECTS AND BASIC TYPES
    1.22 -        return "<Column %s>"%(str(self.MyIndex()))
    1.23 -
    1.24 -
    1.25 -
    1.26  
    1.27  class Block(Alignment):
    1.28      """Block of alignment.

     2.1 --- a/sequence_based_blocks_search/blocks_finder.py	Fri Jul 08 16:20:20 2011 +0400
     2.2 +++ b/sequence_based_blocks_search/blocks_finder.py	Fri Jul 08 18:30:04 2011 +0400
     2.3 @@ -3,7 +3,8 @@
     2.4  import sys
     2.5  sys.path.append("../")
     2.6  from allpy import protein
     2.7 -from allpy markups import *
     2.8 +from allpy.markups import *
     2.9 +from allpy.homology import *
    2.10  import copy
    2.11  import math
    2.12  from functional_groups import functional_groups
    2.13 @@ -340,17 +341,17 @@
    2.14      """returns MonomerHomology object, given alignment
    2.15      with links created by create_links function"""
    2.16      #creating markup
    2.17 -    for sequence in alignment:
    2.18 +    for sequence in alignment.sequences:
    2.19          sim=SequenceIndexMarkup(sequence)
    2.20          sim.refresh()
    2.21      #inferring classes_of_equivalence = homologous monomers = connected_components from links
    2.22      output = MonomerHomology()
    2.23      class_number = 0
    2.24      for column in alignment.columns:
    2.25 -        remaining_sequences = copy.copy(column.sequences)
    2.26 -        while remaining_sequences!=0:
    2.27 +        remaining_sequences = copy.copy(column.keys())
    2.28 +        while remaining_sequences!=[]:
    2.29              connected_component = find_connected_component(remaining_sequences, column)
    2.30 -            if connected_component = []:
    2.31 +            if connected_component == []:
    2.32                  #create class for each of the remaining monomers
    2.33                  for sequence in remaining_sequences:
    2.34                      subset_of_sequences_in_column2monomer_homology_data(output, class_number, [sequence], column)