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src/c/o/cogent-1.5.3/cogent/core/usage.py   cogent(Download)
from cogent.maths.stats.special import fix_rounding_error
from cogent.util.array import euclidean_distance
from cogent.util.misc import Delegator, FunctionWrapper, InverseDict
from cogent.core.genetic_code import GeneticCodes, GeneticCode as GenCodeClass
from cogent.core.info import Info as InfoClass
class InfoFreqs(Freqs, Delegator):
    """Like Freqs, but has an Info object storing additional data.
 
    Intended for holding base or codon frequencies that come from a 
    particular sequence, so that the Info of the sequence can be preserved
class PositionalBaseUsage(Delegator):
    """Stores a BaseUsage for each of the three codon positions."""
 
    def __init__(self, First=None, Second=None, Third=None, Info=None):
        """Returns new PositionalBaseUsage with values for the 3 positions."""

src/p/y/pycogent-HEAD/cogent/core/usage.py   pycogent(Download)
from cogent.maths.stats.special import fix_rounding_error
from cogent.util.array import euclidean_distance
from cogent.util.misc import Delegator, FunctionWrapper, InverseDict
from cogent.core.genetic_code import GeneticCodes, GeneticCode as GenCodeClass
from cogent.core.info import Info as InfoClass
class InfoFreqs(Freqs, Delegator):
    """Like Freqs, but has an Info object storing additional data.
 
    Intended for holding base or codon frequencies that come from a 
    particular sequence, so that the Info of the sequence can be preserved
class PositionalBaseUsage(Delegator):
    """Stores a BaseUsage for each of the three codon positions."""
 
    def __init__(self, First=None, Second=None, Third=None, Info=None):
        """Returns new PositionalBaseUsage with values for the 3 positions."""

src/c/o/cogent-1.5.3/cogent/core/info.py   cogent(Download)
"""
from cogent.parse.record import MappedRecord
from cogent.util.misc import Delegator, FunctionWrapper, ConstrainedDict
 
__author__ = "Rob Knight"
class Info(MappedRecord, Delegator):
    """Dictionary that stores attributes for Sequence objects.
 
    Delegates to DbRefs for database IDs.
    """

src/p/y/pycogent-HEAD/cogent/core/info.py   pycogent(Download)
"""
from cogent.parse.record import MappedRecord
from cogent.util.misc import Delegator, FunctionWrapper, ConstrainedDict
 
__author__ = "Rob Knight"
class Info(MappedRecord, Delegator):
    """Dictionary that stores attributes for Sequence objects.
 
    Delegates to DbRefs for database IDs.
    """

src/c/o/cogent-1.5.3/cogent/maths/matrix/distance.py   cogent(Download)
"""
 
from cogent.util.misc import Delegator
from cogent.util.dict2d import Dict2D
from copy import deepcopy
class DistanceMatrix(Dict2D, Delegator):
    """ 2D dict giving distances from A to B and vice versa """
 
    # default set of amino acids
    RowOrder = list('ACDEFGHIKLMNPQRSTVWY')

src/p/y/pycogent-HEAD/cogent/maths/matrix/distance.py   pycogent(Download)
"""
 
from cogent.util.misc import Delegator
from cogent.util.dict2d import Dict2D
from copy import deepcopy
class DistanceMatrix(Dict2D, Delegator):
    """ 2D dict giving distances from A to B and vice versa """
 
    # default set of amino acids
    RowOrder = list('ACDEFGHIKLMNPQRSTVWY')

src/c/o/cogent-1.5.3/cogent/core/bitvector.py   cogent(Download)
"""
 
from cogent.util.misc import Delegator
import re
from string import maketrans
class MutableBitvector(Delegator):
    """Array of bits (0 or 1) supporting set operations. Supports __setitem__.
    """
    def __init__(self, items='', length=None):
        """Initializes the Bitvector class, storing data in long _vector.

src/p/y/pycogent-HEAD/cogent/core/bitvector.py   pycogent(Download)
"""
 
from cogent.util.misc import Delegator
import re
from string import maketrans
class MutableBitvector(Delegator):
    """Array of bits (0 or 1) supporting set operations. Supports __setitem__.
    """
    def __init__(self, items='', length=None):
        """Initializes the Bitvector class, storing data in long _vector.

src/c/o/cogent-1.5.3/tests/test_util/test_misc.py   cogent(Download)
from cogent.app.util import get_tmp_filename
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import (iterable, max_index, min_index,
    flatten, is_iterable, is_char, is_char_or_noniterable,
    is_str_or_noniterable, not_list_tuple, list_flatten,
class _list_and_string(list, Delegator):
    """Trivial class to demonstrate Delegator.
    """
    def __init__(self, items, string):
        Delegator.__init__(self, string)
    def test_copy(self):
        """copy.copy should work correctly on Delegator"""
        l = ['a']
        d = Delegator(l)
        c = copy(d)
    def test_deepcopy(self):
        """copy.deepcopy should work correctly on Delegator"""
        l = ['a']
        d = Delegator(l)
        c = deepcopy(d)

src/p/y/pycogent-HEAD/tests/test_util/test_misc.py   pycogent(Download)
from cogent.app.util import get_tmp_filename
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import (iterable, max_index, min_index,
    flatten, is_iterable, is_char, is_char_or_noniterable,
    is_str_or_noniterable, not_list_tuple, list_flatten,
class _list_and_string(list, Delegator):
    """Trivial class to demonstrate Delegator.
    """
    def __init__(self, items, string):
        Delegator.__init__(self, string)
    def test_copy(self):
        """copy.copy should work correctly on Delegator"""
        l = ['a']
        d = Delegator(l)
        c = copy(d)
    def test_deepcopy(self):
        """copy.deepcopy should work correctly on Delegator"""
        l = ['a']
        d = Delegator(l)
        c = deepcopy(d)

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