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python-biopython  1.60
Public Member Functions | Static Public Attributes
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet Class Reference
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List of all members.

Public Member Functions

def __repr__
def contains

Static Public Attributes

list letters = ["G", "A", "T", "C", "*"]
dictionary alphabet_matches
 size = None

Detailed Description

Alphabet of a simple Schema for DNA sequences.

This defines a simple alphabet for DNA sequences that has a single
character which can match any other character.

o G,A,T,C - The standard unambiguous DNA alphabet.

o * - Any letter

Definition at line 155 of file Schema.py.


Member Function Documentation

def Bio.Alphabet.Alphabet.__repr__ (   self) [inherited]

Definition at line 21 of file __init__.py.

00021 
00022     def __repr__(self):
00023         return self.__class__.__name__ + "()"

def Bio.Alphabet.Alphabet.contains (   self,
  other 
) [inherited]
Does this alphabet 'contain' the other (OBSOLETE?).

Returns a boolean.  This relies on the Alphabet subclassing
hierarchy only, and does not check the letters property.
This isn't ideal, and doesn't seem to work as intended
with the AlphabetEncoder classes.

Reimplemented in test_GACrossover.TestAlphabet.

Definition at line 24 of file __init__.py.

00024 
00025     def contains(self, other):
00026         """Does this alphabet 'contain' the other (OBSOLETE?).
00027 
00028         Returns a boolean.  This relies on the Alphabet subclassing
00029         hierarchy only, and does not check the letters property.
00030         This isn't ideal, and doesn't seem to work as intended
00031         with the AlphabetEncoder classes."""
00032         return isinstance(other, self.__class__)


Member Data Documentation

Initial value:
{"G" : "G",
                        "A" : "A",
                        "T" : "T",
                        "C" : "C",
                        "*" : "GATC"}

Definition at line 167 of file Schema.py.

list Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters = ["G", "A", "T", "C", "*"] [static]

Reimplemented from Bio.Alphabet.Alphabet.

Definition at line 165 of file Schema.py.

Bio.Alphabet.Alphabet.size = None [static, inherited]

Reimplemented in Bio.Alphabet.ThreeLetterProtein, and Bio.Alphabet.SingleLetterAlphabet.

Definition at line 14 of file __init__.py.


The documentation for this class was generated from the following file: