A B C D E F G H I J K L M N P R S T U W _

A

assort - Variable in class Deme

the correlation in fitness between parents

avgFit - Variable in class Deme

avgRec - Variable in class Deme

B

Bion - class Bion.

The individual reactive biological thingy.

Bion(Deme) - Constructor for class Bion

benMutRate - Variable in class Bion

benMutRate - Variable in class Deme

per locus back mutation rate

bion - Variable in class Deme

C

chunks - Variable in class Bion

correlAB - Variable in class Deme

coupling - Variable in class Deme

cumDist - Variable in class Deme

cumFit - Variable in class Deme

D

Deme - class Deme.

A place with potentially interbreeding, constant population.

Deme(MersenneTwisterFast, int, int, double, double, double, double, double, double, double, double) - Constructor for class Deme

dad - Variable in class Deme

dads - Variable in class Deme

del - Variable in class Bion

delMutRate - Variable in class Bion

delMutRate - Variable in class Deme

per locus mutation rate

delleft - Variable in class Bion

delright - Variable in class Bion

deme - Variable in class Bion

demeGen - Variable in class Deme

drop - Variable in class Deme

E

epistasis - Variable in class Deme

F

fit - Variable in class Bion

fitness(Bion) - Method in class Deme

Whatever fitness function is desired is plugged in here.

flip() - Method in class Deme

juveniles become potentially-reproducing adults

G

GOOD_SEED - Static variable in class MersenneTwister

GOOD_SEED - Static variable in class MersenneTwisterFast

getGamete(Bion) - Method in class Bion

Do recombination, and then mutation to generate a gamete.

getNumEvents(int, double) - Method in class Bion

Choose the appropriate means, pre-computed or not, of generating the number of random events and then return the appropriate value.

getRec() - Method in class Bion

Calculates how many recombination modifiers are present.

H

haveNextNextGaussian - Variable in class MersenneTwisterFast

heapsort(Bion[], int) - Method in class Deme

Heapsort kludged from Numerical Recipes in C.
Used to sort mums and dads by fitness to generate assortativeness.

I

init() - Method in class Bion

Build initial left and right chromosomes and set info fields.

init() - Method in class Deme

Generate pre-computed values, and populate deme with Bions.

initq - Variable in class Deme

initial average frequency of deleterious alleles across fitness loci

isHit - Variable in class Bion

isHit - Variable in class Deme

J

juvCumFit - Variable in class Deme

juvSumFit - Variable in class Deme

juveniles - Variable in class Deme

pre-reproductives

K

k - Variable in class Deme

the constant population size

L

LOWER_MASK - Static variable in class MersenneTwister

LOWER_MASK - Static variable in class MersenneTwisterFast

Loci - class Loci.

Reads the command-line run parameters, creates an instance of Deme and acts as metronome for the run.

Loci() - Constructor for class Loci

lab - Variable in class Bion

left - Variable in class Bion

localSumFit - Variable in class Deme

locals - Variable in class Deme

les habitants

M

M - Static variable in class MersenneTwister

M - Static variable in class MersenneTwisterFast

MATRIX_A - Static variable in class MersenneTwister

MATRIX_A - Static variable in class MersenneTwisterFast

MersenneTwister - class MersenneTwister.

Mersenne Twister and MersenneTwisterFast

MersenneTwister() - Constructor for class MersenneTwister

Constructor using the default seed.

MersenneTwister(long) - Constructor for class MersenneTwister

Constructor using a given seed.

MersenneTwisterFast - class MersenneTwisterFast.

Mersenne Twister and MersenneTwisterFast

MersenneTwisterFast() - Constructor for class MersenneTwisterFast

Constructor using the default seed.

MersenneTwisterFast(long) - Constructor for class MersenneTwisterFast

Constructor using a given seed.

mag01 - Variable in class MersenneTwister

mag01 - Variable in class MersenneTwisterFast

main(String[]) - Static method in class Loci

main(String[]) - Static method in class MersenneTwister

Tests the code.

main(String[]) - Static method in class MersenneTwisterFast

Tests the code.

mateWith(Bion) - Method in class Bion

grab a gamete from each parent, and set info fields

maxDel - Variable in class Deme

minRecRate - Variable in class Bion

minRecRate - Variable in class Deme

per meiosis probability of recombination between any two adjacent loci, without modifiers

modRecRate - Variable in class Bion

modRecRate - Variable in class Deme

the increment in rec rate for homozygote for modifier

mt - Variable in class MersenneTwister

mt - Variable in class MersenneTwisterFast

mti - Variable in class MersenneTwister

mti - Variable in class MersenneTwisterFast

mum - Variable in class Deme

mums - Variable in class Deme

mutateBen(long[], double) - Method in class Bion

uses the global (all-loci) benMutRate

mutateDel(long[], double) - Method in class Bion

uses the global (all-loci) delMutRate

N

N - Static variable in class MersenneTwister

N - Static variable in class MersenneTwisterFast

nAttribs - Variable in class Bion

nAttribs - Variable in class Deme

the number of loci in play, including recombination modifier

next(int) - Method in class MersenneTwister

Returns an integer with bits bits filled with a random number.

nextBoolean() - Method in class MersenneTwister

This method is missing from jdk 1.0.x and below.

nextBoolean(float) - Method in class MersenneTwister

This generates a coin flip with a probability probability of returning true, else returning false.

nextBoolean(double) - Method in class MersenneTwister

This generates a coin flip with a probability probability of returning true, else returning false.

nextBoolean() - Method in class MersenneTwisterFast

nextBoolean(float) - Method in class MersenneTwisterFast

This generates a coin flip with a probability probability of returning true, else returning false.

nextBoolean(double) - Method in class MersenneTwisterFast

This generates a coin flip with a probability probability of returning true, else returning false.

nextByte() - Method in class MersenneTwister

For completeness' sake, though it's not in java.util.Random.

nextByte() - Method in class MersenneTwisterFast

nextBytes(byte[]) - Method in class MersenneTwister

A bug fix for all versions of the JDK.

nextBytes(byte[]) - Method in class MersenneTwisterFast

nextChar() - Method in class MersenneTwister

For completeness' sake, though it's not in java.util.Random.

nextChar() - Method in class MersenneTwisterFast

nextDouble() - Method in class MersenneTwister

A bug fix for versions of JDK 1.1 and below.

nextDouble() - Method in class MersenneTwisterFast

nextFloat() - Method in class MersenneTwister

A bug fix for versions of JDK 1.1 and below.

nextFloat() - Method in class MersenneTwisterFast

nextGaussian() - Method in class MersenneTwister

A bug fix for all JDK code including 1.2.

nextGaussian() - Method in class MersenneTwisterFast

nextGeneration() - Method in class Deme

does viability selection, mating, and stats printout

nextInt(int) - Method in class MersenneTwister

This method is missing from JDK 1.1 and below.

nextInt() - Method in class MersenneTwisterFast

nextInt(int) - Method in class MersenneTwisterFast

Returns an integer drawn uniformly from 0 to n-1.

nextLong() - Method in class MersenneTwisterFast

nextNextGaussian - Variable in class MersenneTwisterFast

nextShort() - Method in class MersenneTwister

For completeness' sake, though it's not in java.util.Random.

nextShort() - Method in class MersenneTwisterFast

np - Variable in class Deme

pre-computed binomial means

numDel - Variable in class Deme

numJuveniles - Variable in class Deme

numLocals - Variable in class Deme

numRec - Variable in class Deme

numSelf - Variable in class Deme

P

pA - Variable in class Deme

pAB - Variable in class Deme

pB - Variable in class Deme

pickParent() - Method in class Deme

The fitter are more likely to be chosen as parents.

poisson(double) - Method in class Bion

found Poisson recipe somewhere: [Calculate exponential.] Set p = exp(-mu), n = 0, q = 1.

prob - Variable in class Deme

R

rab - Variable in class Bion

rand - Variable in class Bion

rand - Variable in class Deme

readObject(ObjectInputStream) - Method in class MersenneTwister

rec - Variable in class Bion

recMask - Variable in class Bion

recRate - Variable in class Deme

recloc - Variable in class Bion

repulsion - Variable in class Deme

right - Variable in class Bion

S

searchCDF(double[], int, double) - Method in class Deme

Binary search to find Cumulative Density Function array element >= target
used for picking parents according to fitness, and
for exact evaluation of the Binomial distribution

selRate - Variable in class Deme

selection coefficient, exact meaning depends on function used in fitness()

setSeed(int[]) - Method in class MersenneTwister

An alternative, more complete, method of seeding the pseudo random number generator.

setSeed(long) - Method in class MersenneTwister

Initalize the pseudo random number generator.

setSeed(int[]) - Method in class MersenneTwisterFast

An alternative, more complete, method of seeding the pseudo random number generator.

setSeed(long) - Method in class MersenneTwisterFast

Initalize the pseudo random number generator.

setSeedOld(long) - Method in class MersenneTwister

Initalize the pseudo random number generator.

setSeedOld(long) - Method in class MersenneTwisterFast

Initalize the pseudo random number generator.

sqrnpq - Variable in class Deme

pre-computed binomial std dev

sumAB() - Method in class Bion

Calculate bits of information having to do with allele correlation and match-up.

sumDel() - Method in class Bion

Calculate number of deleterious alleles on each chromosome, and the total.

T

TEMPERING_MASK_B - Static variable in class MersenneTwister

TEMPERING_MASK_B - Static variable in class MersenneTwisterFast

TEMPERING_MASK_C - Static variable in class MersenneTwister

TEMPERING_MASK_C - Static variable in class MersenneTwisterFast

tAB - Variable in class Bion

tAB - Variable in class Deme

tAb - Variable in class Bion

tAb - Variable in class Deme

taB - Variable in class Bion

taB - Variable in class Deme

tab - Variable in class Bion

tab - Variable in class Deme

toString() - Method in class Bion

totben - Variable in class Deme

totm - Static variable in class Deme

totmut - Variable in class Deme

totr - Static variable in class Deme

totrec - Variable in class Deme

U

UPPER_MASK - Static variable in class MersenneTwister

UPPER_MASK - Static variable in class MersenneTwisterFast

W

writeObject(ObjectOutputStream) - Method in class MersenneTwister

_

__haveNextNextGaussian - Variable in class MersenneTwister

__nextNextGaussian - Variable in class MersenneTwister

A B C D E F G H I J K L M N P R S T U W _