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

Class LocalAlignmentAlgorithm

                object --+    
                         |    
AbstractAlignmentAlgorithm --+
                             |
                            LocalAlignmentAlgorithm

Smith-Waterman local sequence alignment.

Nested Classes
Inherited from `AbstractAlignmentAlgorithm`: `__metaclass__`

Instance Methods

__init__(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57..., gap=-1)
x.__init__(...) initializes x; see help(type(x)) for signature source code

Inherited from AbstractAlignmentAlgorithm: align

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

Class Variables
	START = `0`
	__abstractmethods__ = `frozenset([])`

Properties

Inherited from AbstractAlignmentAlgorithm: gap, scoring_matrix

Inherited from object: __class__

Method Details

init(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57`...`, gap=-1)
(Constructor)

source code

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

Parameters:

scoring - scoring matrix
gap - simple gap penalty

Overrides: object.__init__

(inherited documentation)

Class LocalAlignmentAlgorithm

__init__(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57..., gap=-1) (Constructor)

init(self, scoring=<csb.bio.sequence.alignment.IdentityMatrix object at 0x7fe0c57`...`, gap=-1)
(Constructor)