Back to index

python-biopython  1.60
Public Member Functions | Public Attributes
Bio.pairwise2.affine_penalty Class Reference

List of all members.

Public Member Functions

def __init__
def __call__

Public Attributes

 extend
 penalize_extend_when_opening

Detailed Description

affine_penalty(open, extend[, penalize_extend_when_opening]) -> gap_fn

Create a gap function for use in an alignment.

Definition at line 794 of file pairwise2.py.


Constructor & Destructor Documentation

def Bio.pairwise2.affine_penalty.__init__ (   self,
  open,
  extend,
  penalize_extend_when_opening = 0 
)

Definition at line 800 of file pairwise2.py.

00800 
00801     def __init__(self, open, extend, penalize_extend_when_opening=0):
00802         if open > 0 or extend > 0:
00803             raise ValueError("Gap penalties should be non-positive.")
00804         self.open, self.extend = open, extend
        self.penalize_extend_when_opening = penalize_extend_when_opening

Member Function Documentation

def Bio.pairwise2.affine_penalty.__call__ (   self,
  index,
  length 
)

Definition at line 805 of file pairwise2.py.

00805 
00806     def __call__(self, index, length):
00807         return calc_affine_penalty(
00808             length, self.open, self.extend, self.penalize_extend_when_opening)

Here is the call graph for this function:


Member Data Documentation

Definition at line 803 of file pairwise2.py.

Definition at line 804 of file pairwise2.py.


The documentation for this class was generated from the following file: