1.1 --- a/lib/block.py	Sun Oct 24 10:59:38 2010 +0400
     1.2 +++ b/lib/block.py	Sun Oct 24 11:42:21 2010 +0400
     1.3 @@ -18,6 +18,8 @@
     1.4      *   self.positions -- sorted list of positions of the project.alignment that
     1.5          are included in the block
     1.6      
     1.7 +    Don't change self.sequences -- it may be a link to other block.sequences
     1.8 +    
     1.9      How to create a new block:
    1.10      >>> import project
    1.11      >>> import block
    1.12 @@ -32,7 +34,7 @@
    1.13          if positions==None, all positions are used
    1.14          """
    1.15          if sequences == None:
    1.16 -            sequences = copy(project.sequences)
    1.17 +            sequences = set(project.sequences) # copy
    1.18          if positions == None:
    1.19              positions = range(len(project))
    1.20          self.project = project
    1.21 @@ -106,7 +108,7 @@
    1.22                  if len(clique - set(GC.positions)) < ac_new_atoms * len(clique):
    1.23                      break
    1.24              else:
    1.25 -                GCs.append(Block(self.project, copy(self.sequences), clique))
    1.26 +                GCs.append(Block(self.project, self.sequences, clique))
    1.27                  if ac_count != -1 and len(GCs) >= ac_count:
    1.28                      break
    1.29          return GCs