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

Class IdentityMatrix

           object --+    
                    |    
AbstractScoringMatrix --+
                        |
                       IdentityMatrix

Simple identity-based scoring matrix.

Nested Classes
Inherited from `AbstractScoringMatrix`: `__metaclass__`

Instance Methods

__init__(self, match=1, mismatch=-1)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

float

score(self, x, y)
Return the pairwise score of residues x and y. source code

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

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
float	match Score for a match
float	mismatch Score for a mismatch
Inherited from `object`: `__class__`

Method Details

init(self, match=1, mismatch=-1)
(Constructor)

source code

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

Parameters:

match (float) - score for a match
mismatch (float) - score for a mismatch

Overrides: object.__init__

(inherited documentation)

score(self, x, y)

source code

Return the pairwise score of residues x and y. x and y must be comparable (e.g. implement __eq__ and __hash__).

Parameters:

x - first residue
y - second residue

Returns: float

Raises:

ResidueNotFoundError - if x or y cannot be handled by this scoring matrix

Overrides: AbstractScoringMatrix.score

(inherited documentation)

Property Details

match

Score for a match

Get Method:: unreachable.match(self) - Score for a match
Type:: float

mismatch

Score for a mismatch

Get Method:: unreachable.mismatch(self) - Score for a mismatch
Type:: float

Class IdentityMatrix

__init__(self, match=1, mismatch=-1) (Constructor)

score(self, x, y)

match

mismatch

init(self, match=1, mismatch=-1)
(Constructor)