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

A

addInt(Vector<Integer>) - Method in class World
Adds an interaction to the matrix I
age - Variable in class Organism
The age of the organism counted in updates
avg - Static variable in class World
The number of updates the efficiency is averaged over

B

bitflipProb - Variable in class World
The bit flip probability of inflowing strings
blockEntropy(int) - Method in class BString
Calculates the block entropy of string B
BString - Class in <Unnamed>
The BString class represents the bit strings on which the organisms feed.
BString(boolean[]) - Constructor for class BString
Creates a string from a given bit sequence
BString(boolean[], Vector<Integer>) - Constructor for class BString
Creates a string from a given bit sequence and metabolic history
BString(int, double, int) - Constructor for class BString
Creates a string with a given length of certain type with bitflips

C

change(int) - Method in class BString
Applies a Cellular Automaton rule to the string once and returns the modified string
clearTag() - Method in class Organism
Clear the isNew tag
cloneString() - Method in class BString
Deep-copy of the string
currentGID - Static variable in class Organism
The current highest genotype ID
currentOID - Static variable in class Organism
The current highest organism ID

D

dE - Variable in class Organism
The most recent entropy change achieved by the organism
deltaE(BString, int) - Method in class BString
Calculates difference in entropy between this string and and another string
divide() - Method in class Organism
Creates a daughter organism under mutations.

E

Entropy(int) - Method in class BString
Calculates the approximation of the entropy S of a string B
entropyLevel - Variable in class World
The level of entropy calculation
equals(BString) - Method in class BString
Compares two strings

F

fakeUpdate() - Method in class World
Updates all organisms in the population without carrying out the actual divisions
fixedString - Variable in class World
In the case of fixed strings this is the inflowing string
flow - Variable in class World
The flow rate of bit strings

G

G - Variable in class Organism
The CA rule implemented by the organism, i.e. its pheno/genotype
get(int) - Method in class BString
Returns bit at position i
getAge() - Method in class Organism
Get the age of the organism
getAvgAge() - Method in class World
The average age of the organisms
getAvgEntropy() - Method in class World
The average entropy of bit strings
getAvgIO() - Method in class World
The average IO (entropy difference) of the organisms
getAvgProd() - Method in class World
The average amount of energy that has been extracted from the bit strings.
getAvgStringAge() - Method in class World
The average age of the bit strings.
getCurrentGID() - Static method in class Organism
Returns a GID
getCurrentOID() - Static method in class Organism
Returns an OID
getDivides() - Method in class World
The total number of organism divisions that have occured in the system
getEff() - Method in class World
The average efficiency of the organisms, defined as the average IO divided by the maximum amount of energy that can be extracted from the strings
getFraction() - Method in class BString
Returns the fraction of ones in the string
getFraction(int) - Method in class World
The fraction of the population that corresponds to a given rule
getGenome() - Method in class Organism
Get the organism genotype
getGID() - Method in class Organism
Returns the organism genotype ID number
getHistory() - Method in class BString
Returns metabolic history
getIO(int) - Method in class World
The average IO (entropy difference) of organisms of a certain genotype
getLatestIO() - Method in class Organism
Get the most recent entropy difference
getNextGID() - Static method in class Organism
Returns a GID and increments the counter
getNextOID() - Static method in class Organism
Returns an OID and increments the counter
getNoPhenotypes(double) - Method in class World
The number of genotypes/rules that exist above a certain threshold
getOID() - Method in class Organism
Returns the OID
getOrigString() - Method in class Organism
Get the backup string attached to the organism
getState() - Method in class World
Returns the species distribution
getString() - Method in class Organism
Get the string attached to the organism
GID - Variable in class Organism
The organism genotype identity number.

H

H - Variable in class BString
The metabolic history of the string

I

inEntropy - Variable in class World
The entropy of the inflowing strings
Inoculate(int[], double[]) - Method in class World
Setting the rule frequency to defined values
interactions - Variable in class World
The matrix holding interactions between the species.
IO(World, BString) - Method in class Organism
Swaps the current string and creates a backup
isMutated() - Method in class Organism
Check if the organism is mutated
isNew - Variable in class Organism
Shows if the organism is a newborn

L

length - Variable in class BString
The length of the string

M

main(String[]) - Static method in class Simulation
 
manipulate(int) - Method in class BString
Applies a Cellular Automaton rule to the string once
mutated - Variable in class Organism
Shows if the organism was a mutant at birth
mutated(boolean) - Method in class Organism
Mark the organism as mutated

N

noDivisions - Variable in class World
Counter for the number of organism divisions
noStringsFlowing - Variable in class World
Counter for the number of bit strings flowing into the system

O

OID - Variable in class Organism
The organism identity number (unique to each instance of the class)
Organism - Class in <Unnamed>
The Organism class represents the organisms in the simulation.
Organism(int, int, int) - Constructor for class Organism
Creates an Organism with given properties
organisms - Variable in class World
A Vector containing all the organisms in the World

P

pc - Static variable in class Organism
The copy mutation probability
printString() - Method in class BString
Prints the string to Std.out
productivity - Variable in class World
An array that holds of the productivity for the last avg time steps

R

radiate(double) - Method in class BString
Induce random bitflips, not really used
randomMode - Variable in class World
When strings are random this declares the type of strings being used
randomStrings - Variable in class World
True if random bit strings are used
resources - Variable in class World
A Vector containing all the bit strings in the World

S

S - Variable in class BString
The bit sequence
S - Variable in class Organism
The bit string attached to the organism
S0 - Variable in class Organism
A backup copy of the bit string attached to the organism
saveEff(String) - Method in class World
Saves the average efficiency in a data file
saveFoodEntropy(int) - Method in class World
Saves the entropy of all strings to a data file parametrised by time
saveFoodHistory(int) - Method in class World
Saves the metablic history of all strings to a data file parametrised by time
saveGenotypes(int, double) - Method in class World
Saves all genotypes above a certain fraction to a data file parametrised by time
saveInts(String) - Method in class World
Saves the interaction matrix interactions in a data file
saveState(String) - Method in class World
Saves the no. of organisms in each species (rule) in a data file
saveStats(String, String) - Method in class World
Saves any information in a data file
setEntLevel(int) - Method in class World
Sets the level at which the entropy is calculated
setFlow(double) - Method in class World
Sets the flow rate
setGenome(int) - Method in class Organism
Sets the organism genotype
setGID(int) - Method in class Organism
Sets the organism genotype ID number
setMutRate(double) - Static method in class Organism
Sets the mutation rate
setMutRate(double) - Method in class World
Sets the mutation rate
setOID(int) - Method in class Organism
Sets the organism ID number
setString(BString) - Method in class Organism
Attaches a new bit string to the organism and creates a backup
Simulation - Class in <Unnamed>
This class contains the main-method.
Simulation() - Constructor for class Simulation
 
stringLength - Variable in class World
The length of the bit strings
swapString(BString) - Method in class World
Swaps the specified bit string with a random string from the resource pool

T

test(BString) - Method in class Organism
Manipulates a test string and returns it

U

update(int) - Method in class Organism
Updates the organism
update() - Method in class World
Updates all organisms in the population, takes care of the swapping of strings, and calls the divide method of Organism

W

World - Class in <Unnamed>
The World class represents the world in which the simulation takes place.
World(int, int, int, double, double, int, int) - Constructor for class World
Creates a World with a flow of random strings
World(int, int, double, boolean[], int) - Constructor for class World
Creates a World with a flow of fixed strings

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