"
Template:Team:Amsterdam/maarten/scripts/models
From 2012.igem.org
(Created page with "<html> <script type='text/javascript'> var numeric = (typeof exports === "undefined")?(function numeric() {}):(exports); if(typeof global !== "undefined") { global.numeric = nume...") |
|
| (One intermediate revision not shown) | |
Latest revision as of 20:22, 23 July 2012
//
// Math.seedrandom('yipee'); Sets Math.random to a function that is
// initialized using the given explicit seed.
//
// Math.seedrandom(); Sets Math.random to a function that is
// seeded using the current time, dom state,
// and other accumulated local entropy.
// The generated seed string is returned.
//
// Math.seedrandom('yowza', true);
// Seeds using the given explicit seed mixed
// together with accumulated entropy.
//
//
// Seeds using physical random bits downloaded
// from random.org.
//
// Seeds using urandom bits from call.jsonlib.com,
// which is faster than random.org.
//
// Examples:
//
// Math.seedrandom("hello"); // Use "hello" as the seed.
// document.write(Math.random()); // Always 0.5463663768140734
// document.write(Math.random()); // Always 0.43973793770592234
// var rng1 = Math.random; // Remember the current prng.
//
// var autoseed = Math.seedrandom(); // New prng with an automatic seed.
// document.write(Math.random()); // Pretty much unpredictable.
//
// Math.random = rng1; // Continue "hello" prng sequence.
// document.write(Math.random()); // Always 0.554769432473455
//
// Math.seedrandom(autoseed); // Restart at the previous seed.
// document.write(Math.random()); // Repeat the 'unpredictable' value.
//
// Notes:
//
// Each time seedrandom('arg') is called, entropy from the passed seed
// is accumulated in a pool to help generate future seeds for the
// zero-argument form of Math.seedrandom, so entropy can be injected over
// time by calling seedrandom with explicit data repeatedly.
//
// On speed - This javascript implementation of Math.random() is about
// 3-10x slower than the built-in Math.random() because it is not native
// code, but this is typically fast enough anyway. Seeding is more expensive,
// especially if you use auto-seeding. Some details (timings on Chrome 4):
//
// Our Math.random() - avg less than 0.002 milliseconds per call
// seedrandom('explicit') - avg less than 0.5 milliseconds per call
// seedrandom('explicit', true) - avg less than 2 milliseconds per call
// seedrandom() - avg about 38 milliseconds per call
//
// LICENSE (BSD):
//
// Copyright 2010 David Bau, all rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of this module nor the names of its contributors may
// be used to endorse or promote products derived from this software
// without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
/**
* All code is in an anonymous closure to keep the global namespace clean.
*
* @param {number=} overflow
* @param {number=} startdenom
*/
// Patched by Seb so that seedrandom.js does not pollute the Math object.
// My tests suggest that doing Math.trouble = 1 makes Math lookups about 5%
// slower.
numeric.seedrandom = { pow:Math.pow, random:Math.random };
(function (pool, math, width, chunks, significance, overflow, startdenom) {
//
// seedrandom()
// This is the seedrandom function described above.
//
math['seedrandom'] = function seedrandom(seed, use_entropy) {
var key = [];
var arc4;
// Flatten the seed string or build one from local entropy if needed.
seed = mixkey(flatten(
use_entropy ? [seed, pool] :
arguments.length ? seed :
[new Date().getTime(), pool, window], 3), key);
// Use the seed to initialize an ARC4 generator.
arc4 = new ARC4(key);
// Mix the randomness into accumulated entropy.
mixkey(arc4.S, pool);
// Override Math.random
// This function returns a random double in [0, 1) that contains
// randomness in every bit of the mantissa of the IEEE 754 value.
math['random'] = function random() { // Closure to return a random double:
var n = arc4.g(chunks); // Start with a numerator n < 2 ^ 48
var d = startdenom; // and denominator d = 2 ^ 48.
var x = 0; // and no 'extra last byte'.
while (n < significance) { // Fill up all significant digits by
n = (n + x) * width; // shifting numerator and
d *= width; // denominator and generating a
x = arc4.g(1); // new least-significant-byte.
}
while (n >= overflow) { // To avoid rounding up, before adding
n /= 2; // last byte, shift everything
d /= 2; // right using integer math until
x >>>= 1; // we have exactly the desired bits.
}
return (n + x) / d; // Form the number within [0, 1).
};
// Return the seed that was used
return seed;
};
//
// ARC4
//
// An ARC4 implementation. The constructor takes a key in the form of
// an array of at most (width) integers that should be 0 <= x < (width).
//
// The g(count) method returns a pseudorandom integer that concatenates
// the next (count) outputs from ARC4. Its return value is a number x
// that is in the range 0 <= x < (width ^ count).
//
/** @constructor */
function ARC4(key) {
var t, u, me = this, keylen = key.length;
var i = 0, j = me.i = me.j = me.m = 0;
me.S = [];
me.c = [];
// The empty key [] is treated as [0].
if (!keylen) { key = [keylen++]; }
// Set up S using the standard key scheduling algorithm.
while (i < width) { me.S[i] = i++; }
for (i = 0; i < width; i++) {
t = me.S[i];
j = lowbits(j + t + key[i % keylen]);
u = me.S[j];
me.S[i] = u;
me.S[j] = t;
}
// The "g" method returns the next (count) outputs as one number.
me.g = function getnext(count) {
var s = me.S;
var i = lowbits(me.i + 1); var t = s[i];
var j = lowbits(me.j + t); var u = s[j];
s[i] = u;
s[j] = t;
var r = s[lowbits(t + u)];
while (--count) {
i = lowbits(i + 1); t = s[i];
j = lowbits(j + t); u = s[j];
s[i] = u;
s[j] = t;
r = r * width + s[lowbits(t + u)];
}
me.i = i;
me.j = j;
return r;
};
// For robust unpredictability discard an initial batch of values.
// See http://www.rsa.com/rsalabs/node.asp?id=2009
me.g(width);
}
//
// flatten()
// Converts an object tree to nested arrays of strings.
//
/** @param {Object=} result
* @param {string=} prop
* @param {string=} typ */
function flatten(obj, depth, result, prop, typ) {
result = [];
typ = typeof(obj);
if (depth && typ == 'object') {
for (prop in obj) {
if (prop.indexOf('S') < 5) { // Avoid FF3 bug (local/sessionStorage)
try { result.push(flatten(obj[prop], depth - 1)); } catch (e) {}
}
}
}
return (result.length ? result : obj + (typ != 'string' ? '\0' : ''));
}
//
// mixkey()
// Mixes a string seed into a key that is an array of integers, and
// returns a shortened string seed that is equivalent to the result key.
//
/** @param {number=} smear
* @param {number=} j */
function mixkey(seed, key, smear, j) {
seed += ''; // Ensure the seed is a string
smear = 0;
for (j = 0; j < seed.length; j++) {
key[lowbits(j)] =
lowbits((smear ^= key[lowbits(j)] * 19) + seed.charCodeAt(j));
}
seed = '';
for (j in key) { seed += String.fromCharCode(key[j]); }
return seed;
}
//
// lowbits()
// A quick "n mod width" for width a power of 2.
//
function lowbits(n) { return n & (width - 1); }
//
// The following constants are related to IEEE 754 limits.
//
startdenom = math.pow(width, chunks);
significance = math.pow(2, significance);
overflow = significance * 2;
//
// When seedrandom.js is loaded, we immediately mix a few bits
// from the built-in RNG into the entropy pool. Because we do
// not want to intefere with determinstic PRNG state later,
// seedrandom will not call math.random on its own again after
// initialization.
//
mixkey(math.random(), pool);
// End anonymous scope, and pass initial values.
}(
[], // pool: entropy pool starts empty
numeric.seedrandom, // math: package containing random, pow, and seedrandom
256, // width: each RC4 output is 0 <= x < 256
6, // chunks: at least six RC4 outputs for each double
52 // significance: there are 52 significant digits in a double
));
/* This file is a slightly modified version of quadprog.js from Alberto Santini.
* It has been slightly modified by Sébastien Loisel to make sure that it handles
* 0-based Arrays instead of 1-based Arrays.
* License is in resources/LICENSE.quadprog */
(function(exports) {
function base0to1(A) {
if(typeof A !== "object") { return A; }
var ret = [], i,n=A.length;
for(i=0;i
