Package csb :: Package bio :: Package sequence :: Class SequenceAlphabets |
[frames] | no frames]

# Class SequenceAlphabets

source code

    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=., ...>}