Package Bio :: Module mathfns
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Source Code for Module Bio.mathfns

 1  # Copyright 2000 by Jeffrey Chang.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """This provides useful general math tools (DEPRECATED). 
 7   
 8  This module is considered to be deprecated, and is likely to be removed in a 
 9  future release of Biopython.  Its C code implementation has already been 
10  removed. Please get in touch via the mailing list if this will affect you. 
11   
12  Functions: 
13  fcmp       Compare two floating point numbers, up to a specified precision. 
14  intd       Represent a floating point number as an integer. 
15  safe_log   log, but returns an arbitrarily small number for log(0). 
16  safe_exp   exp, but returns a large or small number instead of overflows. 
17   
18  """ 
19  import warnings 
20  warnings.warn("Bio.mathfns and its C code equivalent Bio.cmathfns are" \ 
21                +" deprecated, and will be removed in a future release of"\ 
22                +" Biopython.  If you want to continue to use this code,"\ 
23                +" please get in contact with the Biopython developers via"\ 
24                +" the mailing lists to avoid its permanent removal from"\ 
25                +" Biopython.", \ 
26                DeprecationWarning) 
27   
28  import math 
29   
30 -def fcmp(x, y, precision):
31 """fcmp(x, y, precision) -> -1, 0, or 1""" 32 if math.fabs(x-y) < precision: 33 return 0 34 elif x < y: 35 return -1 36 return 1
37
38 -def intd(x, digits_after_decimal=0):
39 """intd(x[, digits_after_decimal]) -> int x, rounded 40 41 Represent a floating point number with some digits after the 42 decimal point as an integer. This is useful when floating point 43 comparisons are failing due to precision problems. e.g. 44 intd(5.35, 1) -> 54. 45 46 """ 47 precision = 10.**digits_after_decimal 48 if x >= 0: 49 x = int(x * precision + 0.5) 50 else: 51 x = int(x * precision - 0.5) 52 return x
53
54 -def safe_log(n, zero=None, neg=None):
55 """safe_log(n, zero=None, neg=None) -> log(n) 56 57 Calculate the log of n. If n is 0, returns the value of zero. If n is 58 negative, returns the value of neg. 59 60 """ 61 if n < 0: 62 return neg 63 elif n < 1E-100: 64 return zero 65 return math.log(n)
66 67 LOG2 = math.log(2)
68 -def safe_log2(n, zero=None, neg=None):
69 """safe_log2(n, zero=None, neg=None) -> log(n) 70 71 Calculate the log base 2 of n. If n is 0, returns the value of 72 zero. If n is negative, returns the value of neg. 73 74 """ 75 l = safe_log(n, zero=zero, neg=neg) 76 if l is None: 77 return l 78 return l/LOG2
79
80 -def safe_exp(n, under=None, over=None):
81 """safe_exp(n, under=None, over=None) -> e**n 82 83 Guaranteed not to overflow. Instead of overflowing, it returns 84 the values of 'under' for underflows or 'over' for overflows. 85 86 """ 87 try: 88 return math.exp(n) 89 except OverflowError: 90 if n < 0: 91 return under 92 return over 93 raise "How did I get here?"
94