allpy

diff allpy/base.py @ 310:9ad22a1848fc
Added calls to super to all classes in allpy.base The calls are not exactly correct. This WILL fail in certain inheritance situations. There are two bad situations: * inheritance from object; __init__ of object does not accept any arguments, so it is not compatible with interface of any of our classes * inheritance of Block(Alignment). The situation here is relatively easy to fix: we should force compatibility of function interfaces for Block and Alignment.
author: Daniil Alexeyevsky <me.dendik@gmail.com>
date: Thu, 16 Dec 2010 21:08:03 +0300
parents: 0c3c1856113a
children: 734db2702a5b
     1.1 --- a/allpy/base.py	Thu Dec 16 20:47:09 2010 +0300
     1.2 +++ b/allpy/base.py	Thu Dec 16 21:08:03 2010 +0300
     1.3 @@ -36,6 +36,7 @@
     1.4      instance_type = None
     1.5  
     1.6      def __init__(self, name="", code1="", code3="", is_modified=False):
     1.7 +        super(MonomerType, self).__init__()
     1.8          self.name = name.capitalize()
     1.9          self.code1 = code1.upper()
    1.10          self.code3 = code3.upper()
    1.11 @@ -106,6 +107,7 @@
    1.12      monomer_type = MonomerType
    1.13  
    1.14      def __init__(self, type):
    1.15 +        super(Monomer, self).__init__()
    1.16          self.type = type
    1.17  
    1.18      @classmethod
    1.19 @@ -358,6 +360,7 @@
    1.20          In both cases we use exactly the list used in alignment, thus, if new
    1.21          sequences or columns are added to alignment, the block tracks this too.
    1.22          """
    1.23 +        super(Block, self).__init__()
    1.24          if sequences is None:
    1.25              sequences = alignment.sequences
    1.26          if colums is None:
author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Thu, 16 Dec 2010 21:08:03 +0300
parents	0c3c1856113a
children	734db2702a5b