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[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / Alphabet / IUPAC.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Alphabet/IUPAC.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Alphabet/IUPAC.py
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--- a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Alphabet/IUPAC.py
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-# Copyright 2000-2001 by Andrew Dalke.
-# Revisions copyright 2008 by Peter Cock.
-# All rights reserved.
-# This code is part of the Biopython distribution and governed by its
-# license.  Please see the LICENSE file that should have been included
-# as part of this package.
-
-"""Standard nucleotide and protein alphabets defined by IUPAC."""
-
-from Bio import Alphabet
-from Bio.Data import IUPACData
-
-##################### Protein
-
-# From the IUPAC definition at:
-#   http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html#AA21
-
-assert IUPACData.extended_protein_letters == IUPACData.extended_protein_letters.upper()
-class ExtendedIUPACProtein(Alphabet.ProteinAlphabet):
-    """Extended uppercase IUPAC protein single letter alphabet including X etc.
-
-    In addition to the standard 20 single letter protein codes, this includes:
-    
-    B = "Asx";  Aspartic acid (R) or Asparagine (N)
-    X = "Xxx";  Unknown or 'other' amino acid
-    Z = "Glx";  Glutamic acid (E) or Glutamine (Q)
-    J = "Xle";  Leucine (L) or Isoleucine (I), used in mass-spec (NMR)
-    U = "Sec";  Selenocysteine
-    O = "Pyl";  Pyrrolysine
-
-    This alphabet is not intended to be used with X for Selenocysteine
-    (an ad-hoc standard prior to the IUPAC adoption of U instead).
-    """
-    letters = IUPACData.extended_protein_letters
-
-extended_protein = ExtendedIUPACProtein()
-
-assert IUPACData.protein_letters == IUPACData.protein_letters.upper()
-class IUPACProtein(ExtendedIUPACProtein):
-    """Uppercase IUPAC protein single letter alphabet of the 20 standard amino acids."""
-    letters = IUPACData.protein_letters
-
-protein = IUPACProtein()
-
-##################### DNA
-
-# The next two are the IUPAC definitions, from:
-#   http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html
-class IUPACAmbiguousDNA(Alphabet.DNAAlphabet):
-    """Uppercase IUPAC ambiguous DNA."""
-    letters = IUPACData.ambiguous_dna_letters
-
-ambiguous_dna = IUPACAmbiguousDNA()
-
-class IUPACUnambiguousDNA(IUPACAmbiguousDNA):
-    """Uppercase IUPAC unambiguous DNA (letters GATC only)."""
-    letters = IUPACData.unambiguous_dna_letters
-
-unambiguous_dna = IUPACUnambiguousDNA()
-
-
-# Also from the URL, but not part of the standard
-class ExtendedIUPACDNA(Alphabet.DNAAlphabet):
-    """Extended IUPAC DNA alphabet.
-
-    In addition to the standard letter codes GATC, this includes:
-
-    B = 5-bromouridine
-    D = 5,6-dihydrouridine
-    S = thiouridine
-    W = wyosine
-    """
-    letters = IUPACData.extended_dna_letters
-
-extended_dna = ExtendedIUPACDNA()
-
-##################### RNA
-
-class IUPACAmbiguousRNA(Alphabet.RNAAlphabet):
-    """Uppercase IUPAC ambiguous RNA."""
-    letters = IUPACData.ambiguous_rna_letters
-
-ambiguous_rna = IUPACAmbiguousRNA()
-
-class IUPACUnambiguousRNA(IUPACAmbiguousRNA):
-    """Uppercase IUPAC unambiguous RNA (letters GAUC only)."""
-    letters = IUPACData.unambiguous_rna_letters
-
-unambiguous_rna = IUPACUnambiguousRNA()
-
-# are there extended forms?
-#class ExtendedIUPACRNA(Alphabet.RNAAlphabet):
-#    letters = extended_rna_letters
-#    #   B == 5-bromouridine
-#    #   D == 5,6-dihydrouridine
-#    #   S == thiouridine
-#    #   W == wyosine
-
-
-# We need to load the property resolution information, but we need to
-# wait until after the systems have been loaded. (There's a nasty loop
-# where, eg, translation objects need an alphabet, which need to be
-# assocated with translators.)
-
-from Bio.PropertyManager import default_manager
-
-def _bootstrap(manager, klass, property):
-    assert manager is default_manager
-    del default_manager.class_resolver[IUPACProtein]
-    del default_manager.class_resolver[ExtendedIUPACProtein]
-    del default_manager.class_resolver[IUPACAmbiguousDNA]
-    del default_manager.class_resolver[IUPACUnambiguousDNA]
-    del default_manager.class_resolver[ExtendedIUPACDNA]
-    del default_manager.class_resolver[IUPACAmbiguousRNA]
-    del default_manager.class_resolver[IUPACUnambiguousRNA]
-
-    from Bio.Encodings import IUPACEncoding
-
-    return manager.resolve_class(klass, property)
-
-default_manager.class_resolver[IUPACProtein] = _bootstrap
-default_manager.class_resolver[ExtendedIUPACProtein] = _bootstrap
-default_manager.class_resolver[IUPACAmbiguousDNA] = _bootstrap
-default_manager.class_resolver[IUPACUnambiguousDNA] = _bootstrap
-default_manager.class_resolver[ExtendedIUPACDNA] = _bootstrap
-default_manager.class_resolver[IUPACAmbiguousRNA] = _bootstrap
-default_manager.class_resolver[IUPACUnambiguousRNA] = _bootstrap