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[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / mathfns.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/mathfns.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/mathfns.py
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--- a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/mathfns.py
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-# Copyright 2000 by Jeffrey Chang.  All rights reserved.
-# This code is part of the Biopython distribution and governed by its
-# license.  Please see the LICENSE file that should have been included
-# as part of this package.
-
-"""This provides useful general math tools (DEPRECATED).
-
-This module and its C code equivalent are considered to be deprecated, and
-are likely to be removed in a future release of Biopython.  Please get in
-touch via the mailing list if this will affect you.
-
-Functions:
-fcmp       Compare two floating point numbers, up to a specified precision.
-intd       Represent a floating point number as an integer.
-safe_log   log, but returns an arbitrarily small number for log(0).
-safe_exp   exp, but returns a large or small number instead of overflows.
-
-"""
-import warnings
-warnings.warn("Bio.mathfns and its C code equivalent Bio.cmathfns are" \
-              +" deprecated, and will be removed in a future release of"\
-              +" Biopython.  If you want to continue to use this code,"\
-              +" please get in contact with the Biopython developers via"\
-              +" the mailing lists to avoid its permanent removal from"\
-              +" Biopython.", \
-              DeprecationWarning)
-
-import math
-
-def fcmp(x, y, precision):
-    """fcmp(x, y, precision) -> -1, 0, or 1"""
-    if math.fabs(x-y) < precision:
-        return 0
-    elif x < y:
-        return -1
-    return 1
-
-def intd(x, digits_after_decimal=0):
-    """intd(x[, digits_after_decimal]) -> int x, rounded
-
-    Represent a floating point number with some digits after the
-    decimal point as an integer.  This is useful when floating point
-    comparisons are failing due to precision problems.  e.g.
-    intd(5.35, 1) -> 54.
-
-    """
-    precision = 10.**digits_after_decimal
-    if x >= 0:
-        x = int(x * precision + 0.5)
-    else:
-        x = int(x * precision - 0.5)
-    return x
-
-def safe_log(n, zero=None, neg=None):
-    """safe_log(n, zero=None, neg=None) -> log(n)
-
-    Calculate the log of n.  If n is 0, returns the value of zero.  If n is
-    negative, returns the value of neg.
-
-    """
-    if n < 0:
-        return neg
-    elif n < 1E-100:
-        return zero
-    return math.log(n)
-
-LOG2 = math.log(2)
-def safe_log2(n, zero=None, neg=None):
-    """safe_log2(n, zero=None, neg=None) -> log(n)
-
-    Calculate the log base 2 of n.  If n is 0, returns the value of
-    zero.  If n is negative, returns the value of neg.
-
-    """
-    l = safe_log(n, zero=zero, neg=neg)
-    if l is None:
-        return l
-    return l/LOG2
-
-def safe_exp(n, under=None, over=None):
-    """safe_exp(n, under=None, over=None) -> e**n
-
-    Guaranteed not to overflow.  Instead of overflowing, it returns
-    the values of 'under' for underflows or 'over' for overflows.
-
-    """
-    try:
-        return math.exp(n)
-    except OverflowError:
-        if n < 0:
-            return under
-        return over
-    raise "How did I get here?"
-
-# Try and load C implementations of functions.  If I can't,
-# then just ignore and use the pure python implementations.
-try:
-    from cmathfns import *
-except ImportError:
-    pass