Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / globplot / 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