Package csb :: Package bio :: Package sequence :: Class AlignedSequenceAdapter

Class AlignedSequenceAdapter

     object --+    
              |    
SequenceAdapter --+
                  |
                 AlignedSequenceAdapter

Adapter, which wraps a gapped AbstractSequence object and makes it compatible with the MSA row/entry interface, expected by AbstractAlignment.

The adapter.residues property operates with an UngappedSequenceIndexer, which provides a gap-free view of the underlying sequence.

The adapter.columns property operates with a standard ColumnIndexer, the same indexer which is used to provide the column view in multiple alignments. Adapted sequences therefore act as alignment rows and allow for MSA-column-oriented indexing.

Instance Methods

__getitem__(self, index)

source code

__init__(self, sequence)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

__iter__(self)

source code

int

map_column(self, column)
Return the ungapped sequence rank corresponding to the specified MSA column number. source code

int

map_residue(self, rank)
Return the MSA column number corresponding to the specified ungapped sequence rank. source code

Inherited from SequenceAdapter: __repr__, __str__, extract, strip, subregion

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Properties
ColumnIndexer	columns Provides 1-based access to the respective columns in the MSA.
UngappedSequenceIndexer	residues Provides 1-based access to the residues of the unaligned (ungapped) sequence.
Inherited from `SequenceAdapter`: `alphabet`, `header`, `id`, `length`, `sequence`, `type` Inherited from `object`: `__class__`

Method Details

getitem(self, index)
(Indexing operator)

source code

Overrides: SequenceAdapter.__getitem__

init(self, sequence)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

sequence (AbstractSequence) - adaptee

Overrides: object.__init__

(inherited documentation)

iter(self)

source code

Overrides: SequenceAdapter.__iter__

map_column(self, column)

source code

Return the ungapped sequence rank corresponding to the specified MSA column number.

Parameters:

column (int) - 1-based alignment column number

Returns: int

map_residue(self, rank)

source code

Return the MSA column number corresponding to the specified ungapped sequence rank.

Parameters:

rank (int) - 1-based residue rank

Returns: int

Property Details

columns

Provides 1-based access to the respective columns in the MSA.

Get Method:: unreachable.columns(self) - Provides 1-based access to the respective columns in the MSA.
Type:: ColumnIndexer

residues

Provides 1-based access to the residues of the unaligned (ungapped) sequence.

Get Method:: unreachable.residues(self) - Provides 1-based access to the residues of the unaligned (ungapped) sequence.
Type:: UngappedSequenceIndexer

Class AlignedSequenceAdapter

__getitem__(self, index) (Indexing operator)

__init__(self, sequence) (Constructor)

__iter__(self)

map_column(self, column)

map_residue(self, rank)

columns

residues

getitem(self, index)
(Indexing operator)

init(self, sequence)
(Constructor)

iter(self)