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 (OBSOLETE). 
 7   
 8  This module and its C code equivalent are considered to be obsolete, and 
 9  are likely to be deprecated in a future release of Biopython, before being 
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 math 
20   
21 -def fcmp(x, y, precision):
22 """fcmp(x, y, precision) -> -1, 0, or 1""" 23 if math.fabs(x-y) < precision: 24 return 0 25 elif x < y: 26 return -1 27 return 1
28
29 -def intd(x, digits_after_decimal=0):
30 """intd(x[, digits_after_decimal]) -> int x, rounded 31 32 Represent a floating point number with some digits after the 33 decimal point as an integer. This is useful when floating point 34 comparisons are failing due to precision problems. e.g. 35 intd(5.35, 1) -> 54. 36 37 """ 38 precision = 10.**digits_after_decimal 39 if x >= 0: 40 x = int(x * precision + 0.5) 41 else: 42 x = int(x * precision - 0.5) 43 return x
44
45 -def safe_log(n, zero=None, neg=None):
46 """safe_log(n, zero=None, neg=None) -> log(n) 47 48 Calculate the log of n. If n is 0, returns the value of zero. If n is 49 negative, returns the value of neg. 50 51 """ 52 if n < 0: 53 return neg 54 elif n < 1E-100: 55 return zero 56 return math.log(n)
57 58 LOG2 = math.log(2)
59 -def safe_log2(n, zero=None, neg=None):
60 """safe_log2(n, zero=None, neg=None) -> log(n) 61 62 Calculate the log base 2 of n. If n is 0, returns the value of 63 zero. If n is negative, returns the value of neg. 64 65 """ 66 l = safe_log(n, zero=zero, neg=neg) 67 if l is None: 68 return l 69 return l/LOG2
70
71 -def safe_exp(n, under=None, over=None):
72 """safe_exp(n, under=None, over=None) -> e**n 73 74 Guaranteed not to overflow. Instead of overflowing, it returns 75 the values of 'under' for underflows or 'over' for overflows. 76 77 """ 78 try: 79 return math.exp(n) 80 except OverflowError: 81 if n < 0: 82 return under 83 return over 84 raise "How did I get here?"
85 86 # Try and load C implementations of functions. If I can't, 87 # then just ignore and use the pure python implementations. 88 try: 89 from cmathfns import * 90 except ImportError: 91 pass 92