Package csb :: Package bio :: Package sequence :: Class SequenceAlphabets

Class SequenceAlphabets

object --+
         |
        SequenceAlphabets

Sequence alphabet enumerations.

Note: This class is kept for backwards compatibility. The individual alphabet classes must be defined in the top level namespace, otherwise the new enum types cannot be pickled properly.

Nested Classes
	Nucleic Nucleic sequence alphabet
	Protein Protein sequence alphabet
	StdProtein Standard protein sequence alphabet
	Unknown Unknown sequence alphabet

Instance Methods
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__init__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Static Methods

bool

contains(alphabet)
Return True if alphabet is a sequence alphabet source code

csb.core.enum

get(type)
Get the alphabet corresponding to the specified sequence type source code

Class Variables
	ALL_ALPHABETS = `set([<ProteinAlphabet: ILE=I, GLN=Q, ...>, <Un...`
	MAP = `{DNA: <NucleicAlphabet: NotT=V, Purine=R, ...>, NucleicA...`

Properties
Inherited from `object`: `__class__`

Method Details

contains(alphabet)
Static Method

source code

Return True if alphabet is a sequence alphabet

Parameters:

alphabet (csb.core.enum)

Returns: bool

get(type)
Static Method

source code

Get the alphabet corresponding to the specified sequence type

Parameters:

type (csb.core.EnumItem) - a member of SequenceTypes

Returns: csb.core.enum

Class Variable Details

ALL_ALPHABETS

Value:

set([<ProteinAlphabet: ILE=I, GLN=Q, ...>,
     <UnknownAlphabet: UNK=X, INSERTION=., ...>,
     <NucleicAlphabet: NotT=V, Purine=R, ...>])

MAP

Value:

{DNA: <NucleicAlphabet: NotT=V, Purine=R, ...>,
 NucleicAcid: <NucleicAlphabet: NotT=V, Purine=R, ...>,
 Protein: <ProteinAlphabet: ILE=I, GLN=Q, ...>,
 RNA: <NucleicAlphabet: NotT=V, Purine=R, ...>,
 Unknown: <UnknownAlphabet: UNK=X, INSERTION=., ...>}

Class SequenceAlphabets

contains(alphabet) Static Method

get(type) Static Method

ALL_ALPHABETS

MAP

contains(alphabet)
Static Method

get(type)
Static Method