Package csb :: Package bio :: Package sequence :: Module alignment :: Class AbstractAlignmentAlgorithm

Class AbstractAlignmentAlgorithm

object --+
         |
        AbstractAlignmentAlgorithm

Known Subclasses:

Base class for all sequence alignment algorithms.

This class was designed with simple sequence alignment algorithms in mind. Implementors have full control over the behavior of the scoring function and the dynamic programming matrix, but implementing things that require additional matrices (such as affine gap penalties) might be trickier.

Nested Classes
	__metaclass__ Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods

__init__(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57..., gap=0)
x.__init__(...) initializes x; see help(type(x)) for signature source code

AlignmentResult

align(self, query, subject)
Align two sequences and return the optimal alignment.

source code

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

Class Variables
	__abstractmethods__ = `frozenset(['_expandable', '_initialize',...`

Properties
float	gap Simple gap penalty
AbstractScoringMatrix	scoring_matrix Scoring matrix
Inherited from `object`: `__class__`

Method Details

init(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57`...`, gap=0)
(Constructor)

source code

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

Parameters:

scoring (AbstractScoringMatrix) - scoring matrix
gap (float) - simple gap penalty

Overrides: object.__init__

(inherited documentation)

align(self, query, subject)

source code

Align two sequences and return the optimal alignment.

Parameters:

query (AbstractSequence) - first sequence
subject (AbstractSequence) - second sequence

Returns: AlignmentResult

Class Variable Details

abstractmethods

Value:

frozenset(['_expandable', '_initialize', '_max', '_terminus'])

Property Details

gap

Simple gap penalty

Get Method:: unreachable.gap(self) - Simple gap penalty
Type:: float

scoring_matrix

Scoring matrix

Get Method:: unreachable.scoring_matrix(self) - Scoring matrix
Type:: AbstractScoringMatrix

Class AbstractAlignmentAlgorithm

__init__(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57..., gap=0) (Constructor)

align(self, query, subject)

__abstractmethods__

gap

scoring_matrix

init(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57`...`, gap=0)
(Constructor)

abstractmethods