1.1 --- a/allpy/base.py	Tue Feb 01 18:46:23 2011 +0300
     1.2 +++ b/allpy/base.py	Tue Feb 01 23:08:08 2011 +0300
     1.3 @@ -4,6 +4,9 @@
     1.4  import util
     1.5  import fasta
     1.6  
     1.7 +# import this very module as means of having all related classes in one place
     1.8 +import base
     1.9 +
    1.10  default_gaps = set((".", "-", "~"))
    1.11  """Set of characters to recoginze as gaps when parsing alignment."""
    1.12  
    1.13 @@ -13,6 +16,9 @@
    1.14      type = None
    1.15      """Either of 'dna', 'rna', 'protein'."""
    1.16  
    1.17 +    types = base
    1.18 +    """Mapping of related types. SHOULD be redefined in subclasses."""
    1.19 +
    1.20      by_code1 = {}
    1.21      """A mapping from 1-letter code to Monomer subclass."""
    1.22  
    1.23 @@ -90,14 +96,10 @@
    1.24      *   source -- str denoting source of the sequence
    1.25  
    1.26      Any of them may be empty (i.e. hold empty string)
    1.27 -
    1.28 -    Class attributes:
    1.29 -
    1.30 -    *   monomer_type -- type of monomers in sequence, must be redefined when
    1.31 -        subclassing
    1.32      """
    1.33  
    1.34 -    monomer_type = Monomer
    1.35 +    types = base
    1.36 +    """Mapping of related types. SHOULD be redefined in subclasses."""
    1.37  
    1.38      name = ''
    1.39      description = ''
    1.40 @@ -118,7 +120,7 @@
    1.41      @classmethod
    1.42      def from_string(cls, string, name='', description='', source=''):
    1.43          """Create sequences from string of one-letter codes."""
    1.44 -        monomer = cls.monomer_type.from_code1
    1.45 +        monomer = cls.types.Monomer.from_code1
    1.46          monomers = [monomer(letter) for letter in string]
    1.47          return cls.from_monomers(monomers, name, description, source)
    1.48  
    1.49 @@ -136,16 +138,8 @@
    1.50  class Alignment(object):
    1.51      """Alignment. It is a list of Columns."""
    1.52  
    1.53 -    alignment_type = None
    1.54 -    """Related Alignment class. SHOULD be redefined when subclassing."""
    1.55 -    # Actually given value at EOF, since name Alignment is not yet defined
    1.56 -
    1.57 -    block_type = None
    1.58 -    """Related Block class. SHOULD be redefined when subclassing."""
    1.59 -    # Actually given value at EOF, since name Block is not yet defined
    1.60 -
    1.61 -    sequence_type = Sequence
    1.62 -    """Type of sequences in alignment. SHOULD be redefined when subclassing."""
    1.63 +    types = base
    1.64 +    """Mapping of related types. SHOULD be redefined in subclasses."""
    1.65  
    1.66      sequences = None
    1.67      """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
    1.68 @@ -171,7 +165,7 @@
    1.69      def append_row_from_string(self, string,
    1.70              name='', description='', source='', gaps=default_gaps):
    1.71          """Add row from a string of one-letter codes and gaps. Return self."""
    1.72 -        Sequence = self.sequence_type
    1.73 +        Sequence = self.types.Sequence
    1.74          not_gap = lambda (i, char): char not in gaps
    1.75          without_gaps = util.remove_each(string, gaps)
    1.76          sequence = Sequence.from_string(without_gaps, name, description, source)
    1.77 @@ -392,6 +386,9 @@
    1.78      the column.
    1.79      """
    1.80  
    1.81 +    types = base
    1.82 +    """Mapping of related types. SHOULD be redefined in subclasses."""
    1.83 +
    1.84      def __hash__(self):
    1.85          """Return hash by identity."""
    1.86          return id(self)
    1.87 @@ -434,7 +431,4 @@
    1.88          block.columns = columns
    1.89          return block
    1.90  
    1.91 -Alignment.alignment_type = Alignment
    1.92 -Alignment.block_type = Block
    1.93 -
    1.94  # vim: set ts=4 sts=4 sw=4 et:

     2.1 --- a/allpy/dna.py	Tue Feb 01 18:46:23 2011 +0300
     2.2 +++ b/allpy/dna.py	Tue Feb 01 23:08:08 2011 +0300
     2.3 @@ -1,25 +1,24 @@
     2.4  import base
     2.5  import data.codes
     2.6  
     2.7 +import dna
     2.8 +
     2.9  class Monomer(base.Monomer):
    2.10      """DNA monomers: nucleotides."""
    2.11      type = 'dna'
    2.12 +    types = dna
    2.13      by_code1 = {}
    2.14      by_code3 = {}
    2.15      by_name = {}
    2.16  Monomer._initialize(data.codes.dna)
    2.17  
    2.18  class Sequence(base.Sequence):
    2.19 -    monomer_type = Monomer
    2.20 +    types = dna
    2.21 +
    2.22 +class Alignment(base.Alignment):
    2.23 +    types = dna
    2.24  
    2.25  class Block(Alignment, base.Block):
    2.26      pass
    2.27  
    2.28 -class Alignment(base.Alignment):
    2.29 -    sequence_type = Sequence
    2.30 -    block_type = Block
    2.31 -    # alignment_type is defined at EOF, since name Alignment undefined yet
    2.32 -
    2.33 -Alignment.alignment_type = Alignment
    2.34 -
    2.35  # vim: set ts=4 sts=4 sw=4 et:

     3.1 --- a/allpy/protein.py	Tue Feb 01 18:46:23 2011 +0300
     3.2 +++ b/allpy/protein.py	Tue Feb 01 23:08:08 2011 +0300
     3.3 @@ -1,9 +1,12 @@
     3.4  import base
     3.5  import data.codes
     3.6  
     3.7 +import protein
     3.8 +
     3.9  class Monomer(base.Monomer):
    3.10      """Protein monomers: aminoacids."""
    3.11      type = 'protein'
    3.12 +    types = protein
    3.13      by_code1 = {}
    3.14      by_code3 = {}
    3.15      by_name = {}
    3.16 @@ -14,15 +17,13 @@
    3.17      pass
    3.18  
    3.19  class Sequence(base.Sequence):
    3.20 -    monomer_type = Monomer
    3.21 +    types = protein
    3.22  
    3.23  class Block(Alignment, base.Block):
    3.24      pass
    3.25  
    3.26  class Alignment(base.Alignment):
    3.27 -    sequence_type = Sequence
    3.28 -    block_type = Block
    3.29 -    # alignment_type is defined at EOF, since name Alignment undefined yet
    3.30 +    types = protein
    3.31  
    3.32      def muscle_align(self):
    3.33          """ Simple align ths alignment using sequences (muscle)
    3.34 @@ -52,6 +53,4 @@
    3.35                      self.body[sequence].append(old_monomer)
    3.36          os.unlink(tmp_file.name)
    3.37  
    3.38 -Alignment.alignment_type = Alignment
    3.39 -
    3.40  # vim: set ts=4 sts=4 sw=4 et:

     4.1 --- a/allpy/rna.py	Tue Feb 01 18:46:23 2011 +0300
     4.2 +++ b/allpy/rna.py	Tue Feb 01 23:08:08 2011 +0300
     4.3 @@ -1,25 +1,24 @@
     4.4  import base
     4.5  import data.codes
     4.6  
     4.7 +import rna
     4.8 +
     4.9  class Monomer(base.Monomer):
    4.10      """RNA monomers: nucleotides."""
    4.11      type = 'rna'
    4.12 +    types = rna
    4.13      by_code1 = {}
    4.14      by_code3 = {}
    4.15      by_name = {}
    4.16  Monomer._initialize(data.codes.rna)
    4.17  
    4.18  class Sequence(base.Sequence):
    4.19 -    monomer_type = Monomer
    4.20 +    types = rna
    4.21  
    4.22  class Block(Alignment, base.Block):
    4.23      pass
    4.24  
    4.25  class Alignment(base.Alignment):
    4.26 -    sequence_type = Sequence
    4.27 -    block_type = Block
    4.28 -    # alignment_type is defined at EOF, since name Alignment undefined yet
    4.29 -
    4.30 -Alignment.alignment_type = Alignment
    4.31 +    types = rna
    4.32  
    4.33  # vim: set ts=4 sts=4 sw=4 et: