A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

actionPerformed(ActionEvent) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
add - Static variable in class mar.virtualmachine.MarVM
 
Add - class physis.core.task.math.Add.
 
ADD - Static variable in class arche.UP
 
add() - Method in class mar.virtualmachine.MarVM
 
Add() - Constructor for class physis.core.task.math.Add
 
add(int, int, int) - Method in class arche.UP
 
ADD1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
ADD2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
ADD3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
Add3Args - class physis.core.task.math.Add3Args.
 
Add3Args() - Constructor for class physis.core.task.math.Add3Args
 
ADD4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
addend - Static variable in class physis.core.random.JavaUtilRandom
 
addStorage(Storage) - Method in class arche.StorageArray
Structural elements can be added step-by-step.
addTrigger(Trigger) - Method in class physis.core.triggers.Triggers
 
adjustIP(int) - Method in class psoup.virtualmachine.PrimordialSoupVM
The instruction pointer-register is incremented.
adjustPeriodicalSchedule() - Method in class physis.core.triggers.TriggerImpl
This method shoulb be invoked after execution if the trigger is periodical.
age - Variable in class physis.core.DigitalOrganismImpl
The age of the organism in updates.
AGE - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
AGE_COMM - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
alien - Variable in class physis.core.virtualmachine.PhysisVirtualMachine
This is another codetape for alien genomes.
allocate - Static variable in class mar.virtualmachine.MarVM
 
ALLOCATE - Static variable in class arche.UP
 
allocate() - Method in class mar.virtualmachine.MarVM
 
allocate(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
allocate(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
It's a biological operator.
allocate(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
It's a biological operator.
allocate(int) - Method in class arche.UP
Allocates memory with the specified size.
allocated_size - Variable in class physis.core.virtualmachine.SoupGeneticCodeTape
 
alltasks - Variable in class physis.core.task.TaskLibrary
Contains all of the tasks in the order of instantiation.
alreadyallocated - Variable in class physis.core.virtualmachine.SoupGeneticCodeTape
 
alreadyallocated - Variable in class physis.core.virtualmachine.CellGeneticCodeTape
It's a flag which indicates whether an allocation has happened or not.
an_org - Variable in class physis.core.genotype.GeneticSnapshot.Data
 
AND - Static variable in class arche.UP
 
and(int, int, int) - Method in class arche.UP
 
arche - package arche
The implementation of the ARCHE processor, which is similar to the Universal Turing Machine but it's more like a real-life processor.
Array2DDigitalOrganismIterator - class physis.core.iterator.Array2DDigitalOrganismIterator.
Enumerates organisms from a two-dimensional array.
Array2DDigitalOrganismIterator(DigitalOrganism[][]) - Constructor for class physis.core.iterator.Array2DDigitalOrganismIterator
 
ArrayDigitalOrganismIterator - class physis.core.iterator.ArrayDigitalOrganismIterator.
Enumerates organisms from an array.
ArrayDigitalOrganismIterator(DigitalOrganism[]) - Constructor for class physis.core.iterator.ArrayDigitalOrganismIterator
 
attributes - Static variable in class physis.core.virtualmachine.SoupGeneticCodeTape
The attributes array for the memory pool.
attributes - Variable in class physis.core.virtualmachine.CellGeneticCodeTape
Each byte represents the attributes of an instruction.
average_age - Variable in class physis.core.Population
 
average_effective_length - Variable in class physis.core.Population
 
average_fitness - Variable in class physis.core.Population
 
average_genome_length - Variable in class physis.core.Population
 
average_merit - Variable in class physis.core.Population
 
average_time_slice - Static variable in class physis.core.Configuration
Average number of performed VM cycles per update.
AVERAGE_TIME_SLICE - Static variable in class physis.core.Configuration
 
avga - Variable in class physis.core.statistics.StatisticsImpl
 
avga_s - Variable in class physis.core.statistics.StatisticsImpl
 
avgel - Variable in class physis.core.statistics.StatisticsImpl
 
avgel_s - Variable in class physis.core.statistics.StatisticsImpl
 
avgf - Variable in class physis.core.statistics.StatisticsImpl
 
avgf_s - Variable in class physis.core.statistics.StatisticsImpl
 
avggl - Variable in class physis.core.statistics.StatisticsImpl
 
avggl_s - Variable in class physis.core.statistics.StatisticsImpl
 
avgm - Variable in class physis.core.statistics.StatisticsImpl
 
avgm_s - Variable in class physis.core.statistics.StatisticsImpl
 

B

B - Static variable in class arche.UP
Blank (for separating different stacks for example).
bank - Static variable in class physis.core.genotype.GeneBank
Keys are Genomes, values are GenomeDatas.
bearer - Variable in class physis.core.virtualmachine.PhysisVirtualMachine
It's a backreference to the bearer digtal organism.
BEGIN - Static variable in class arche.UP
 
BiologicalEvent - class physis.core.event.BiologicalEvent.
We call some events occuring in this artificial system biological because their role is similar.
BiologicalEvent() - Constructor for class physis.core.event.BiologicalEvent
 
BIRTH_THRESHOLD - Static variable in class physis.core.genotype.GeneBank
 
blank - Static variable in class physis.core.virtualmachine.PhysisVirtualMachine
The blank instruction.
blank_inst - Static variable in class physis.core.virtualmachine.CellGeneticCodeTape
 
BLANK_INSTRUCTION - Static variable in class physis.core.virtualmachine.InstructionSet
The nop instruction should be in all instructionsets.
blockCopy(int, int, int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
blockCopy(int, int, int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Copies an instruction from source position to destination position.
blockCopy(int, int, int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
 
bonusmultiplier - Variable in class physis.core.Merit
 
buildInstructionSet() - Method in class arche.UP
Builds the instrucionset from the tape.
buildLibrary(String) - Method in class physis.core.task.TaskLibrary
Builds the internal datastructure of the task framework.
buildProcessor() - Method in class arche.UP
The main for method for building the processor.
buildStructure(StorageArray) - Method in class arche.UP
Builds the structural elements.
bw - Variable in class physis.core.statistics.StatisticsImpl
 
BY_MAX - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
BY_MAX_EVER_REACHED - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
byte2Mbyte(long, int) - Static method in class physis.log.Log
 

C

calculateEffectiveLength() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
The effective length can be calculated by the number of executed instructions.
calculateEffectiveLength() - Method in interface physis.core.virtualmachine.GeneticCodeTape
The effective length can be calculated by the number of executed instructions.
calculateEffectiveLength() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
The effective length can be calculated by the number of executed instructions.
calculateFitness(int) - Method in class physis.core.Merit
Fitness is calculated by the merit divided by the gestation time.
CDEC - Static variable in class arche.UP
 
cdec(int) - Method in class arche.UP
 
cell_size - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
CellGeneticCodeTape - class physis.core.virtualmachine.CellGeneticCodeTape.
Cell-like implementations of the genetic codetape.
CellGeneticCodeTape(short[], byte[]) - Constructor for class physis.core.virtualmachine.CellGeneticCodeTape
Creates codetape from instructionarray.
CellGeneticCodeTape(String) - Constructor for class physis.core.virtualmachine.CellGeneticCodeTape
It reads the instructions from a file.The first organism is created this way.(One instruction per line, lines beginning with # are discarded.
CellLifeSpace - interface physis.core.lifespace.CellLifeSpace.
Marker interface for cell based lifespaces.
changeBonuses(double) - Method in class physis.core.task.TaskAdapter
 
changeBonuses(double) - Method in interface physis.core.task.Task
Multiplies the bonuses via multiplying the bonus's part above 1.0.
changeBonusesGlobally(int) - Method in class physis.core.task.TaskLibrary
 
ChangeTaskBonusesTrigger - class physis.core.triggers.ChangeTaskBonusesTrigger.
 
ChangeTaskBonusesTrigger() - Constructor for class physis.core.triggers.ChangeTaskBonusesTrigger
 
checkActivity(int[], int[]) - Method in class physis.core.task.TaskAdapter
 
checkActivity(int[], int[]) - Method in interface physis.core.task.Task
Checks an IO activity whether it performs the represented task.
checkActivity(int[], int[]) - Method in class physis.core.task.advanced.Reverse
 
checkActivity(int[], int[]) - Method in class physis.core.task.advanced.Sort
 
checkActivity(int[], int[]) - Method in class physis.core.task.basic.Put
 
checkActivity(int[], int[]) - Method in class physis.core.task.basic.Echo
 
checkActivity(int[], int[]) - Method in class physis.core.task.basic.Get
 
checkActivity(int[], int[]) - Method in class physis.core.task.math.Add3Args
 
checkActivity(int[], int[]) - Method in class physis.core.task.math.Sub
 
checkActivity(int[], int[]) - Method in class physis.core.task.math.Add
 
checkActivity(int[], int[]) - Method in class physis.core.task.math.Double
 
checkActivity(int[], int[]) - Method in class physis.core.task.math.Square
 
checkActivity(int[], int[]) - Method in class physis.core.task.math.Triple
 
checkIOActivity(Metabolism, PerformedTasksRegister) - Method in class physis.core.task.TaskLibrary
Returns the meritmultiplier according to the organism's activity or Zero if it didn't perform any task.
child - Variable in class physis.core.virtualmachine.CellGeneticCodeTape
When the organism is pregnant the child's code is being developed here.
child_loc - Variable in class physis.core.virtualmachine.SoupGeneticCodeTape
The child's position.
child_size - Variable in class physis.core.virtualmachine.SoupGeneticCodeTape
The child's size
childattributes - Variable in class physis.core.virtualmachine.CellGeneticCodeTape
 
CINC - Static variable in class arche.UP
 
cinc(int) - Method in class arche.UP
 
CLEAR - Static variable in class arche.UP
 
clear() - Method in class physis.core.Metabolism
Clears the buffers.
clear() - Method in class physis.core.task.PerformedTasksRegister
 
clear() - Method in class arche.Storage
 
clear() - Method in class arche.Stack
 
clear() - Method in class arche.Register
 
clear() - Method in class arche.Queue
 
clear(int) - Method in class arche.UP
 
clearExecutedFlag(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
clearExecutedFlag(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
 
clearExecutedFlag(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
 
client - Variable in class physis.core.DigitalOrganismProxy
 
CLLB - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
CLLF - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
CodeTape - interface physis.core.virtualmachine.CodeTape.
Simply represents a codetape which has a size (number of contained instructions, length) and one instruction(code) can be retrieved via giving its position.
color_assignmnet_mode - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
colorrange - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
ColorRange - class physis.visualisation.util.ColorRange.
 
colorrange_size - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
ColorRange(Color, Color, int) - Constructor for class physis.visualisation.util.ColorRange
 
ColorRange(int) - Constructor for class physis.visualisation.util.ColorRange
Creates the colorrange with the spektrum from BLUE to RED.
ColorRangePanel - class physis.visualisation.panels.ColorRangePanel.
A simple panel which shows a colorrange vertically.
ColorRangePanel(ColorRange) - Constructor for class physis.visualisation.panels.ColorRangePanel
 
colors - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
colors - Variable in class physis.visualisation.util.ColorRange
 
COMPARE - Static variable in class arche.UP
 
compare(int, int, int) - Method in class arche.UP
Compares the content of the op1 and op2 and the result is stored in the result SE element.
config_file - Static variable in class physis.core.PHYSIS
The name of the file containing the configuration parameters (with full path).
Configuration - class physis.core.Configuration.
This class contains the required parameters for the running system.
Configuration() - Constructor for class physis.core.Configuration
 
ConstantScheduler - class physis.core.scheduler.ConstantScheduler.
This is the simplest scheduling algorithm.
ConstantScheduler() - Constructor for class physis.core.scheduler.ConstantScheduler
 
contains(short) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
contains(short) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Returns true if the codetape contains the specified instruction.
contains(short) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Returns true if the codetape contains the specified instruction.
COPIED - Static variable in interface physis.core.virtualmachine.GeneticCodeTape
Instruction-attribute: the instruction is a copied one.
copy - Static variable in class mar.virtualmachine.MarVM
 
copy_mutation_rate - Variable in class physis.core.EnvironmentImpl
 
COPY_MUTATION_RATE - Static variable in class physis.core.EnvironmentImpl
 
copy() - Method in class mar.virtualmachine.MarVM
 
copy(int, int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
copy(int, int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Copies an instruction from source position to destination position.
copy(int, int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Copies an instruction from source cell to destination cell.
copyShouldBeMutated() - Method in class physis.core.EnvironmentImpl
Answers the question: Should the current copied instruction be mutated?
copyShouldBeMutated() - Method in interface physis.core.Environment
Answers the question: Should the current copied instruction be mutated?
copyShouldBeMutated() - Method in class physis.core.virtualmachine.PhysisVMTracer
Answers the question: Should the current copied instruction be mutated?
count_b - Static variable in class mar.virtualmachine.MarVM
 
count_b() - Method in class mar.virtualmachine.MarVM
 
count_f - Static variable in class mar.virtualmachine.MarVM
 
count_f() - Method in class mar.virtualmachine.MarVM
 
counter - Variable in class physis.core.task.TaskAdapter
 
counter - Variable in class physis.core.virtualmachine.PhysisVirtualMachine
counts the instructions between creating childs
cr - Variable in class physis.visualisation.panels.ColorRangePanel
 
createInstruction(int, int, int) - Method in class arche.UP
Creates the NUMBERth instruction which is on the tape from start to stop.
createMenu() - Method in class physis.visualisation.PhysisGUI
 
createQueue(int) - Static method in class arche.StorageFactory
 
createRegister() - Static method in class arche.StorageFactory
 
createSocket(String) - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
createStack(int) - Static method in class arche.StorageFactory
 

D

DataExtractTrigger - class physis.core.triggers.DataExtractTrigger.
Subclasses can extract some specific information about the population.
DataExtractTrigger() - Constructor for class physis.core.triggers.DataExtractTrigger
 
debug(String) - Static method in class physis.log.Log
 
dec - Static variable in class mar.virtualmachine.MarVM
 
DEC - Static variable in class arche.UP
 
dec() - Method in class mar.virtualmachine.MarVM
 
dec(int) - Method in class arche.UP
Decrements the content of a structural element.
DEC1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
DEC2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
DEC3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
DEC4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
DEFAULT_CELL_SIZE - Static variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
DEFAULT_COLOR_ASSIGNMENT_MODE - Static variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
DEFAULT_COLOR_RANGE_SIZE - Static variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
DEFAULT_SEED - Static variable in class physis.core.random.MersenneTwister
 
DEFAULT_VIEW_MODE - Static variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
delete_rate - Variable in class physis.core.EnvironmentImpl
 
DELETE_RATE - Static variable in class physis.core.EnvironmentImpl
 
delete() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
Removes an instruction from a random position.
delete() - Method in interface physis.core.virtualmachine.GeneticCodeTape
Removes an instruction from a random position.
delete() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Removes an instruction from a random position.
DigitalOrganism - interface physis.core.DigitalOrganism.
A digital organisms are the most important entities in this system.
DigitalOrganismImpl - class physis.core.DigitalOrganismImpl.
Plain implementation of the DigitalOrganism interface.
DigitalOrganismImpl() - Constructor for class physis.core.DigitalOrganismImpl
It simply creates the organism - it doesn't mean it's alive.
DigitalOrganismImpl(String) - Constructor for class physis.core.DigitalOrganismImpl
 
DigitalOrganismIterator - interface physis.core.iterator.DigitalOrganismIterator.
Iterator for digital organisms.
DigitalOrganismProxy - class physis.core.DigitalOrganismProxy.
This class functions as a server.
DigitalOrganismProxy(int, DigitalOrganism[]) - Constructor for class physis.core.DigitalOrganismProxy
 
digorgit - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
dir - Variable in class physis.core.triggers.OrganismExtractTrigger
 
direction - Variable in class arche.UP
The actual direction (the communication partner).
DisasterTrigger - class physis.core.triggers.DisasterTrigger.
 
DisasterTrigger() - Constructor for class physis.core.triggers.DisasterTrigger
 
DistributedLattice2DLifeSpace - class physis.core.lifespace.DistributedLattice2DLifeSpace.
dependency: Array2DDigitalOrganismIterator, ArrayDigitalOrganismIterator
DistributedLattice2DLifeSpace() - Constructor for class physis.core.lifespace.DistributedLattice2DLifeSpace
Creates a lifespace.
DistributedLattice2DLifeSpace(int, int) - Constructor for class physis.core.lifespace.DistributedLattice2DLifeSpace
Creates a lifespace with different with dimension x * y.
DIV - Static variable in class arche.UP
 
div(int, int, int) - Method in class arche.UP
 
divide - Static variable in class mar.virtualmachine.MarVM
 
DIVIDE - Static variable in class arche.UP
 
divide_mutation_rate - Variable in class physis.core.EnvironmentImpl
 
DIVIDE_MUTATION_RATE - Static variable in class physis.core.EnvironmentImpl
 
divide() - Method in class mar.virtualmachine.MarVM
 
divide() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
divide() - Method in interface physis.core.virtualmachine.GeneticCodeTape
It divides the codetape.
divide() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
It divides the codetape.
divide() - Method in class arche.UP
The only one biological operation for cell division.
divideShouldBeMutated() - Method in class physis.core.EnvironmentImpl
Answers the question: Should the current divided codetape be mutated?
divideShouldBeMutated() - Method in interface physis.core.Environment
Answers the question: Should the current divided codetape be mutated?
divideShouldBeMutated() - Method in class physis.core.virtualmachine.PhysisVMTracer
Answers the question: Should the current divided codetape be mutated?
doesExistProperty(String) - Static method in class physis.core.Configuration
Examines whether the given parameter exists or not.
dominant_fitness - Variable in class physis.core.genotype.GeneticSnapshot
 
dominant_org - Variable in class physis.core.genotype.GeneticSnapshot
 
Double - class physis.core.task.math.Double.
 
Double() - Constructor for class physis.core.task.math.Double
 

E

east - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
EAST - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
east_server - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
Echo - class physis.core.task.basic.Echo.
 
Echo() - Constructor for class physis.core.task.basic.Echo
 
effectivelength - Variable in class physis.core.Merit
 
EMPTY - Static variable in class mar.virtualmachine.MarVM
 
end - Variable in class physis.core.triggers.TriggerImpl
 
environment - Static variable in class physis.core.PHYSIS
Mainly for performance reasons this reference can be publicly available this way: PHYSIS.environment
The default environment is EnvironmentImpl is instantiated by PHYSIS.
environment - Variable in class physis.core.triggers.EnvironmentTrigger
Populationtriggers should access the environment, that's why they have the reference.
Environment - interface physis.core.Environment.
The environment of an organism is defined by the surrounding physical world - in Physis: the tasks and the other organisms.
EnvironmentImpl - class physis.core.EnvironmentImpl.
The default implementation for the Environment
EnvironmentImpl() - Constructor for class physis.core.EnvironmentImpl
The constructor is private because it's a singleton.
EnvironmentTrigger - class physis.core.triggers.EnvironmentTrigger.
An environment-trigger can alter the environment of the population during the running.
EnvironmentTrigger() - Constructor for class physis.core.triggers.EnvironmentTrigger
 
equals(Object) - Method in class physis.core.genotype.Genome
This is really important because we don't want to store the same genome twice.
equals(Object) - Method in class physis.core.virtualmachine.Instruction
 
error(Exception) - Static method in class physis.log.Log
 
error(String) - Static method in class physis.log.Log
 
execute() - Method in class mar.virtualmachine.MarVM
Executes the next instruction.
execute() - Method in class physis.core.triggers.TriggerImpl
This method should be overridden by the concrete implementations.
execute() - Method in class physis.core.triggers.OrganismExtractTrigger
 
execute() - Method in class physis.core.triggers.ChangeTaskBonusesTrigger
 
execute() - Method in class physis.core.triggers.DisasterTrigger
 
execute() - Method in interface physis.core.triggers.Trigger
Executes the trigger.
execute() - Method in class physis.core.triggers.GeneticSnapshotTrigger
 
execute() - Method in class physis.core.virtualmachine.VirtualMachine
Calling this method forces the machine to execute the next instruction.
execute() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
execute() - Method in class arche.UP
 
execute(int) - Method in class mar.virtualmachine.MarVM
 
execute(int) - Method in class physis.core.virtualmachine.VirtualMachine
Calling this method forces te VM to execute the next N instructions.
execute(int) - Method in class psoup.virtualmachine.PrimordialSoupVM
 
execute(int) - Method in class arche.UP
 
EXECUTED - Static variable in interface physis.core.virtualmachine.GeneticCodeTape
Instruction-attribute: the instruction is executed at least once.
EXECUTED_OR_COPIED - Static variable in interface physis.core.virtualmachine.GeneticCodeTape
Instruction-attribute: the instruction is executed or copied.
EXPIRATION_TIME - Static variable in class physis.core.genotype.GeneBank
 

F

fetchInst(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
fetchInst(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Simply returns the instruction or operand on the specified position.
fetchInst(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Just returns the value without checking.
filename - Variable in class physis.core.triggers.GeneticSnapshotTrigger
 
fillOperands(int, short[], int) - Method in class arche.UP
 
fillWithOrganisms(DigitalOrganismIterator) - Method in class physis.core.scheduler.ParallelScheduler
 
fillWithOrganisms(DigitalOrganismIterator) - Method in class physis.core.scheduler.ConstantScheduler
 
fillWithOrganisms(DigitalOrganismIterator) - Method in class physis.core.scheduler.MeritScheduler
 
fillWithOrganisms(DigitalOrganismIterator) - Method in interface physis.core.scheduler.Scheduler
Before starting the scheduling process the scheduler has to build up its internal data structure.
fillWithOrganisms(DigitalOrganismIterator) - Method in class physis.core.scheduler.ScaledMeritScheduler
 
fitness - Variable in class physis.core.DigitalOrganismImpl
 
FITNESS - Static variable in class physis.core.DigitalOrganismProxy
 
FITNESS - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
FITNESS_COMM - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
fitness(int) - Method in class physis.core.DigitalOrganismProxy
Writes to the socket the organism's fitness.
flipFromZeroFlag() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
FORK_TH - Static variable in class arche.UP
 
fork_th(int) - Method in class arche.UP
 
FOSSIL_TIME - Static variable in class physis.core.genotype.GeneBank
 
FROMZERO_COMM - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
fromzero_flag - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
FULL - Static variable in class mar.virtualmachine.MarVM
 

G

gatherInformation(long) - Method in class physis.core.statistics.StatisticsImpl
 
gatherInformation(long) - Method in interface physis.core.statistics.Statistics
 
GDIR - Static variable in class arche.UP
 
gdir(int) - Method in class arche.UP
 
GENE_BANK_ENABLED - Static variable in class physis.core.Configuration
 
GENE_BANK_MAXSIZE - Static variable in class physis.core.Configuration
 
GeneBank - class physis.core.genotype.GeneBank.
Stores (dynamically and persistently) the genetic information of the whole population.
genebank_max_size - Static variable in class physis.core.Configuration
 
GeneBank() - Constructor for class physis.core.genotype.GeneBank
 
geneBankEnabled - Static variable in class physis.core.Configuration
 
GeneticCodeTape - interface physis.core.virtualmachine.GeneticCodeTape.
The abstraction of the genetic code.
GeneticCodeTapeFactory - class physis.core.virtualmachine.GeneticCodeTapeFactory.
 
GeneticCodeTapeFactory() - Constructor for class physis.core.virtualmachine.GeneticCodeTapeFactory
 
GeneticSnapshot - class physis.core.genotype.GeneticSnapshot.
This class represents a snapshot about the genetic structure of the population in a timepoint.
GeneticSnapshot.Data - class physis.core.genotype.GeneticSnapshot.Data.
Small inner class for values in the snapshot hashtable.
GeneticSnapshot.Data(GeneticSnapshot) - Constructor for class physis.core.genotype.GeneticSnapshot.Data
 
GeneticSnapshot(DigitalOrganismIterator) - Constructor for class physis.core.genotype.GeneticSnapshot
 
GeneticSnapshotTrigger - class physis.core.triggers.GeneticSnapshotTrigger.
 
GeneticSnapshotTrigger() - Constructor for class physis.core.triggers.GeneticSnapshotTrigger
 
genome - Variable in class physis.core.genotype.Genome
The array containing the instruction codes.
Genome - class physis.core.genotype.Genome.
The genetic information for persistent storage.
Genome(short[]) - Constructor for class physis.core.genotype.Genome
 
GenomeData - class physis.core.genotype.GenomeData.
Some useful information about a genome.
GenomeData(long) - Constructor for class physis.core.genotype.GenomeData
 
GenomeData(long, Genome) - Constructor for class physis.core.genotype.GenomeData
 
gestation_time - Variable in class physis.core.virtualmachine.PhysisVirtualMachine
Time (in executed instructions) needed to create a child.
GESTATION_TIME_INVALID - Static variable in class physis.core.virtualmachine.PhysisVirtualMachine
This value shows that the VM hasn't executed a succesfull divide operation yet.
get - Static variable in class mar.virtualmachine.MarVM
 
Get - class physis.core.task.basic.Get.
 
get() - Method in class mar.virtualmachine.MarVM
 
Get() - Constructor for class physis.core.task.basic.Get
 
getAbundance(String) - Method in class physis.core.genotype.GeneticSnapshot
 
getAge() - Method in class physis.core.DigitalOrganismImpl
 
getAge() - Method in class physis.core.RemoteDigitalOrganism
 
getAge() - Method in interface physis.core.DigitalOrganism
Gives the age of the organism.
getAllOrganism() - Method in class physis.core.Population
 
getAllOrganisms() - Method in class physis.core.lifespace.MemoryPoolLifeSpace
 
getAllOrganisms() - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
This method provides all the organisms of the lifespace.
getAllOrganisms() - Method in interface physis.core.lifespace.LifeSpace
This method provides all the organisms of the lifespace.
getAllOrganisms() - Method in class physis.core.lifespace.Lattice2DLifeSpace
This method provides all the organisms of the lifespace.
getAverageAge() - Method in class physis.core.Population
 
getAverageEffectiveLength() - Method in class physis.core.Population
 
getAverageFitness() - Method in class physis.core.Population
 
getAverageGenomeLength() - Method in class physis.core.Population
 
getAverageMerit() - Method in class physis.core.Population
 
getAverageTimeSlice() - Static method in class physis.core.Configuration
 
getBearer() - Method in class physis.core.virtualmachine.PhysisVirtualMachine
Returns the bearer organism.
getBlankInstrunction() - Method in class physis.core.virtualmachine.InstructionSet
 
getBonusMultiplier() - Method in class physis.core.Merit
 
getBufferSize() - Method in class physis.core.Metabolism
Returns the size of the buffers.
getCellSize() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
getChildGenome() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
Returns the genetic information from the codetape.
getChildGenome() - Method in interface physis.core.virtualmachine.GeneticCodeTape
Returns the genetic information from the child-codetape.
getChildGenome() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Returns the genetic information from the codetape.
getChildInstruction(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
getColor(int) - Method in class physis.visualisation.util.ColorRange
 
getColorAssignmentMode() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
getColorRangeSize() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
getColorShades(Color, Color, int) - Static method in class physis.visualisation.util.ColorRange
 
getCounter() - Method in class physis.core.task.TaskAdapter
 
getCounter() - Method in interface physis.core.task.Task
Gets the value of task counter.
getDeadColor() - Method in class physis.visualisation.util.ColorRange
 
getDominantFitness() - Method in class physis.core.genotype.GeneticSnapshot
 
getDominantGenotype() - Method in class physis.core.genotype.GeneticSnapshot
 
getEast() - Method in interface physis.core.lifespace.Remote2DLattice
 
getEast() - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
getEffectiveLength() - Method in class physis.core.DigitalOrganismImpl
 
getEffectiveLength() - Method in class physis.core.RemoteDigitalOrganism
 
getEffectiveLength() - Method in class physis.core.Merit
 
getEffectiveLength() - Method in interface physis.core.DigitalOrganism
Returns the effective length.
getEffectiveLength() - Method in class physis.core.virtualmachine.PhysisVirtualMachine
Gives the number of copied or executed instructions.
getEffectiveLength() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
getFirst() - Method in interface physis.core.iterator.DigitalOrganismIterator
Returns the first organism.
getFirst() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
getFirst() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
getFitness() - Method in class physis.core.DigitalOrganismImpl
 
getFitness() - Method in class physis.core.RemoteDigitalOrganism
 
getFitness() - Method in interface physis.core.DigitalOrganism
Returns the fitness value of the organism.
getFullTimeStamp() - Static method in class physis.log.Log
 
getGeneBankMaxSize() - Static method in class physis.core.Configuration
 
getGeneticCodeTape(short[], byte[]) - Static method in class physis.core.virtualmachine.GeneticCodeTapeFactory
 
getGeneticCodeTape(String) - Static method in class physis.core.virtualmachine.GeneticCodeTapeFactory
 
getGenome() - Method in class mar.virtualmachine.MarVM
 
getGenome() - Method in class physis.core.DigitalOrganismImpl
 
getGenome() - Method in class physis.core.RemoteDigitalOrganism
 
getGenome() - Method in interface physis.core.DigitalOrganism
Gives the genetic information of the organism.
getGenome() - Method in class physis.core.virtualmachine.PhysisVirtualMachine
Returns the genetic information.
getGenome() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
Returns the genetic information from the codetape.
getGenome() - Method in interface physis.core.virtualmachine.GeneticCodeTape
Returns the genetic information from the codetape.
getGenome() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Returns the genetic information from the codetape.
getGenome() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
getGenome() - Method in class arche.UP
 
getGenomeName(Genome) - Static method in class physis.core.genotype.GeneBank
 
getGenomeSize() - Method in class mar.virtualmachine.MarVM
 
getGenomeSize() - Method in class physis.core.DigitalOrganismImpl
 
getGenomeSize() - Method in class physis.core.RemoteDigitalOrganism
 
getGenomeSize() - Method in interface physis.core.DigitalOrganism
Gives the size of the organism's genome.
getGenomeSize() - Method in class physis.core.virtualmachine.PhysisVirtualMachine
Returns the size of the genome.
getGenomeSize() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
getGenomeSize() - Method in class arche.UP
 
getGestationTime() - Method in class physis.core.virtualmachine.PhysisVirtualMachine
Gives the number of instructions that was needed last time to yield a new organism.
getGroupName() - Method in class physis.core.task.TaskGroup
 
getID() - Method in class physis.core.task.TaskAdapter
 
getID() - Method in interface physis.core.task.Task
Returns the internal ID of the task.
getInputData() - Method in class physis.core.EnvironmentImpl
This provides the input from the environment (~food).
getInputData() - Method in interface physis.core.Environment
This provides the input from the environment (~food).
getInputData() - Method in class physis.core.virtualmachine.PhysisVMTracer
This provides the input from the environment (~food).
getInputs() - Method in class physis.core.Metabolism
Gets the inputvalues in chronological order.
getInputSize() - Method in class physis.core.Metabolism
Returns the number of inputs.
getInputSize() - Method in class physis.core.task.TaskAdapter
 
getInputSize() - Method in interface physis.core.task.Task
Returns the number of input arguments.
getInputSize() - Method in class physis.core.task.advanced.Reverse
 
getInputSize() - Method in class physis.core.task.advanced.Sort
 
getInputSize() - Method in class physis.core.task.basic.Put
 
getInputSize() - Method in class physis.core.task.basic.Echo
 
getInputSize() - Method in class physis.core.task.basic.Get
 
getInputSize() - Method in class physis.core.task.math.Add3Args
 
getInputSize() - Method in class physis.core.task.math.Sub
 
getInputSize() - Method in class physis.core.task.math.Add
 
getInputSize() - Method in class physis.core.task.math.Double
 
getInputSize() - Method in class physis.core.task.math.Square
 
getInputSize() - Method in class physis.core.task.math.Triple
 
getInstance() - Static method in class physis.core.PHYSIS
This returns an instance of the system if the full path of the configuration file is correctly set.
getInstance() - Static method in class physis.core.lifespace.LifeSpaceFactory
 
getInstance() - Static method in class physis.core.virtualmachine.InstructionSet
 
getInstance(String) - Static method in class physis.core.virtualmachine.InstructionSet
 
getInstruction(short) - Method in class physis.core.virtualmachine.InstructionSet
Gives the thin InstructionCode object according to the given instruction_code.
getInstructionByCode(short) - Method in class physis.core.virtualmachine.InstructionSet
 
getInstructionByName(String) - Method in class physis.core.virtualmachine.InstructionSet
 
getInstructionCode() - Method in class physis.core.virtualmachine.Instruction
 
getInstructionCodeRandomly() - Method in class physis.core.virtualmachine.InstructionSet
This method is used when mutating the codetape.
getInstructionMnemonic(short) - Method in class physis.core.virtualmachine.InstructionSet
Gives the instruction's name (mnemonic) corresponding to the given instruction_code.
getJVMInfo() - Static method in class physis.log.Log
 
getLast() - Method in interface physis.core.iterator.DigitalOrganismIterator
Returns the last organism.
getLast() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
getLast() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
getLifeSpace() - Method in class physis.core.EnvironmentImpl
 
getLifeSpace() - Method in interface physis.core.Environment
 
getLifeSpace() - Method in class physis.core.virtualmachine.PhysisVMTracer
 
getMaxAge() - Method in class physis.core.Population
 
getMaxAgeEverReached() - Method in class physis.core.Population
 
getMaxAgeOrganism() - Method in class physis.core.Population
 
getMaxAllocationRatio() - Static method in class physis.core.Configuration
 
getMaxEffectiveLength() - Method in class physis.core.Population
 
getMaxEffectiveLengthEverReached() - Method in class physis.core.Population
 
getMaxEffectiveLengthOrganism() - Method in class physis.core.Population
 
getMaxFitness() - Method in class physis.core.Population
 
getMaxFitnessEverReached() - Method in class physis.core.Population
 
getMaxFitnessOrganism() - Method in class physis.core.Population
 
getMaxGenomeLength() - Method in class physis.core.Population
 
getMaxGenomeLengthEverReached() - Method in class physis.core.Population
 
getMaxGenomeLengthOrganism() - Method in class physis.core.Population
 
getMaxMerit() - Method in class physis.core.Population
 
getMaxMeritEverReached() - Method in class physis.core.Population
 
getMaxMeritOrganism() - Method in class physis.core.Population
 
getMaxNumberOfTasks() - Static method in class physis.core.Configuration
 
getMaxNumberOfUpdates() - Static method in class physis.core.Configuration
 
getMaxTaskSize() - Static method in class physis.core.Configuration
 
getMerit() - Method in class physis.core.DigitalOrganismImpl
 
getMerit() - Method in class physis.core.RemoteDigitalOrganism
 
getMerit() - Method in interface physis.core.DigitalOrganism
Retruns the merit.
getMeritMultiplier(int) - Method in class physis.core.task.TaskAdapter
 
getMeritMultiplier(int) - Method in interface physis.core.task.Task
Returns the merit multiplier when the task is performed.
getMeritValue() - Method in class physis.core.Merit
Merit equals the effective length multipled by the bonuses.
getMetabolism() - Method in class physis.core.DigitalOrganismImpl
 
getMetabolism() - Method in class physis.core.RemoteDigitalOrganism
 
getMetabolism() - Method in interface physis.core.DigitalOrganism
Gives the Metabolism of the organism.
getMetabolism() - Method in class physis.core.event.InteractionEvent
The IObuffer of the organism-environment interaction.
getMinAllocationRatio() - Static method in class physis.core.Configuration
 
getMinFitness() - Method in class physis.core.Population
 
getMinMerit() - Method in class physis.core.Population
 
getMinProliferationRatio() - Static method in class physis.core.Configuration
 
getMnemonic() - Method in class physis.core.virtualmachine.Instruction
Returns the mnemonic (name) of the instruction.
getName() - Method in class physis.core.genotype.GenomeData
 
getName() - Method in class physis.core.task.TaskAdapter
The name equals the class name without the physis.core.task.
getName() - Method in interface physis.core.task.Task
Name specification: groupname_idname_inputnumber_outputnumber
getName() - Method in class physis.core.virtualmachine.InstructionSet
 
getNeighbour() - Method in class physis.core.DigitalOrganismImpl
 
getNeighbour() - Method in class physis.core.RemoteDigitalOrganism
 
getNeighbour() - Method in interface physis.core.DigitalOrganism
Returns the organism's neighbour.
getNeighbourRandomly(DigitalOrganism) - Method in class physis.core.EnvironmentImpl
 
getNeighbourRandomly(DigitalOrganism) - Method in interface physis.core.Environment
Returns one organism of the neighbours of the organism specified by the parameter.
getNeighbourRandomly(DigitalOrganism) - Method in class physis.core.virtualmachine.PhysisVMTracer
 
getNeighbours(DigitalOrganism) - Method in class physis.core.lifespace.MemoryPoolLifeSpace
 
getNeighbours(DigitalOrganism) - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
This method gives the neighbours of an organism.
getNeighbours(DigitalOrganism) - Method in interface physis.core.lifespace.LifeSpace
This method gives the neighbours of an organism.
getNeighbours(DigitalOrganism) - Method in class physis.core.lifespace.Lattice2DLifeSpace
This method gives the neighbours of an organism.
getNewBornColor() - Method in class physis.visualisation.util.ColorRange
 
getNewSeed() - Method in class physis.core.event.ProliferationEvent
The genetic information of the newborn child on a codetape.
getNextSequence() - Static method in class physis.core.genotype.GeneBank
 
getNorth() - Method in interface physis.core.lifespace.Remote2DLattice
 
getNorth() - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
getNumberOfBirths() - Method in class physis.core.genotype.GenomeData
 
getNumberOfCopiedInstructionsInChild() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
 
getNumberOfFertileOrganisms() - Method in class physis.core.Population
Gives the current number of fertile organism in the lifespace.
getNumberOfLivingOrganisms() - Method in class physis.core.Population
Gives the current number of living organism in the lifespace.
getNumberOfOperands() - Method in class physis.core.virtualmachine.Instruction
Returns the number of operands.
getNumberOfRewardedPerforms() - Method in class physis.core.task.TaskAdapter
 
getNumberOfRewardedPerforms() - Method in interface physis.core.task.Task
Not all executions of a task are rewarded.
getNumberOfSpawns() - Method in class physis.core.genotype.GenomeData
 
getNurse() - Static method in class physis.core.nursing.NurseFactory
 
getNurseClassName() - Static method in class physis.core.Configuration
 
getOrganism() - Method in class physis.core.event.BiologicalEvent
Returns the actor organism of the event.
getOrganismRandomly() - Method in class physis.core.lifespace.MemoryPoolLifeSpace
 
getOrganismRandomly() - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
Gives an organism randomly from the entire 'soup'.
getOrganismRandomly() - Method in interface physis.core.lifespace.LifeSpace
Gives an organism randomly from the entire 'soup'.
getOrganismRandomly() - Method in class physis.core.lifespace.Lattice2DLifeSpace
Gives an organism randomly from the entire 'soup'.
getOutputs() - Method in class physis.core.Metabolism
Gets the outputvalues in chronological order.
getOutputSize() - Method in class physis.core.Metabolism
Returns the number of outputs.
getOutputSize() - Method in class physis.core.task.TaskAdapter
 
getOutputSize() - Method in interface physis.core.task.Task
Returns the number of generated values.
getOutputSize() - Method in class physis.core.task.advanced.Reverse
 
getOutputSize() - Method in class physis.core.task.advanced.Sort
 
getOutputSize() - Method in class physis.core.task.basic.Put
 
getOutputSize() - Method in class physis.core.task.basic.Echo
 
getOutputSize() - Method in class physis.core.task.basic.Get
 
getOutputSize() - Method in class physis.core.task.math.Add3Args
 
getOutputSize() - Method in class physis.core.task.math.Sub
 
getOutputSize() - Method in class physis.core.task.math.Add
 
getOutputSize() - Method in class physis.core.task.math.Double
 
getOutputSize() - Method in class physis.core.task.math.Square
 
getOutputSize() - Method in class physis.core.task.math.Triple
 
getPerformedTasks() - Method in class physis.core.DigitalOrganismImpl
 
getPerformedTasks() - Method in class physis.core.RemoteDigitalOrganism
 
getPerformedTasks() - Method in interface physis.core.DigitalOrganism
Gives the container of the performed tasks.
getPerformedTasks() - Method in class physis.core.event.InteractionEvent
The table registering the performed tasks.
getPhysisHome() - Static method in class physis.core.Configuration
 
getPhysisVM() - Static method in class physis.core.virtualmachine.VirtualMachineFactory
Creates a VM for Physis with initial state.
getPhysisVM(String) - Static method in class physis.core.virtualmachine.VirtualMachineFactory
Creates a VM for Physis with initial state.
getPopulation() - Method in class physis.core.PHYSIS
Returns the instance's population.
getPopulationSize() - Method in class physis.core.Population
 
getPositinInfo() - Method in class physis.core.DigitalOrganismImpl
 
getPositinInfo() - Method in class physis.core.RemoteDigitalOrganism
 
getPositinInfo() - Method in interface physis.core.DigitalOrganism
Gives the position information.
getProperty(String) - Static method in class physis.core.Configuration
Provides acces for non-frequently used parameters.
getRandom() - Method in class physis.core.EnvironmentImpl
 
getRandom() - Method in interface physis.core.Environment
The only one random-generator in one Physis-instance should be in the environment.
getRandom() - Method in class physis.core.virtualmachine.PhysisVMTracer
 
getRandomTape(int) - Static method in class physis.core.virtualmachine.CellGeneticCodeTape
 
getRegion(double) - Method in class physis.core.lifespace.MemoryPoolLifeSpace
 
getRegion(double) - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
getRegion(double) - Method in interface physis.core.lifespace.LifeSpace
Returns organisms from a connected local territory in the lifespace.
getRegion(double) - Method in class physis.core.lifespace.Lattice2DLifeSpace
 
getScheduler() - Static method in class physis.core.scheduler.SchedulerFactory
 
getSize() - Method in class physis.core.lifespace.MemoryPoolLifeSpace
 
getSize() - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
Gives the capacity of the lifespace.
getSize() - Method in interface physis.core.lifespace.LifeSpace
Gives the capacity (the number of cells) of the lifespace.
getSize() - Method in class physis.core.lifespace.Lattice2DLifeSpace
Gives the capacity of the lifespace.
getSize() - Method in interface physis.core.virtualmachine.CodeTape
Returns the number of instructions on the tape.
getSize() - Method in class physis.core.virtualmachine.InstructionSet
 
getSize() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
getSize() - Method in interface physis.core.virtualmachine.GeneticCodeTape
Returns the absolute size of the codetape.(number of contained instructions)
getSize() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Returns the size of the codetape.
getSize() - Method in class physis.visualisation.util.ColorRange
 
getSize() - Method in class arche.Storage
Returns the number of cells inside the storage.
getSize() - Method in class arche.Stack
 
getSize() - Method in class arche.Register
Returns the size of the storage element, constant 1 for a register.
getSize() - Method in class arche.Queue
 
getSnapshotSize() - Method in class physis.core.genotype.GeneticSnapshot
 
getSomeOrganisms(double) - Method in class physis.core.lifespace.MemoryPoolLifeSpace
 
getSomeOrganisms(double) - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
getSomeOrganisms(double) - Method in interface physis.core.lifespace.LifeSpace
Returns some organisms.
getSomeOrganisms(double) - Method in class physis.core.lifespace.Lattice2DLifeSpace
 
getSouth() - Method in interface physis.core.lifespace.Remote2DLattice
 
getSouth() - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
getState() - Method in class mar.virtualmachine.MarVM
 
getState() - Method in class physis.core.virtualmachine.VirtualMachine
Returns the String representation of the current state of the virtualmachine including all stacks registers in the architecture and the instruction point by the instructionpointer: etc.
getState() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
getState() - Method in class arche.UP
 
getStatistics(Population) - Static method in class physis.core.statistics.StatisticsFactory
 
getStructuralElements() - Method in class arche.StorageArray
After building-up, it gives back the array of structural elements.
getTask(String, String) - Static method in class physis.core.task.TaskFactory
 
getTaskGroups() - Method in class physis.core.task.TaskLibrary
 
getTaskLibrary() - Method in class physis.core.EnvironmentImpl
Returns the tasklibrary.
getTaskLibrary() - Method in interface physis.core.Environment
The container of the tasks.
getTaskLibrary() - Method in class physis.core.virtualmachine.PhysisVMTracer
Returns the tasklibrary.
getTaskNameByID(int) - Method in class physis.core.task.TaskLibrary
 
getTasks() - Method in class physis.core.task.TaskGroup
 
getTasksFromGroup(String) - Method in class physis.core.task.TaskLibrary
 
getTimeStamp() - Static method in class physis.log.Log
 
getTrigger(String) - Static method in class physis.core.triggers.TriggerFactory
Creating a trigger consists of two steps:
1.
getType() - Method in class physis.core.virtualmachine.Instruction
Returns the type identifier.
getTypeName(int) - Method in class physis.core.virtualmachine.InstructionSet
Gives the name of the corresponding integer type code.
getUpdateCount() - Method in class physis.core.PHYSIS
Returns the number of the current update cycle.
getViewMode() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
getVM() - Method in class physis.core.DigitalOrganismImpl
 
getVM() - Method in class physis.core.RemoteDigitalOrganism
 
getVM() - Method in interface physis.core.DigitalOrganism
Returns the organism's internal virtual machine.
getVM() - Static method in class physis.core.virtualmachine.VirtualMachineFactory
Creates a VM with initial state.
getVMClassName() - Static method in class physis.core.Configuration
 
getWest() - Method in interface physis.core.lifespace.Remote2DLattice
 
getWest() - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
groups_by_names - Variable in class physis.core.task.TaskLibrary
Keys groupnames, values Taskarrays.

H

hashcode - Variable in class physis.core.genotype.Genome
We store the hashcode for performance reasosns.
hashCode() - Method in class physis.core.genotype.Genome
 
hasNext() - Method in interface physis.core.iterator.DigitalOrganismIterator
Returns true if there is at least one organism more.
hasNext() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
hasNext() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
hasNext() - Method in class physis.core.task.TaskIterator
 
hasOperand - Variable in class physis.core.virtualmachine.Instruction
Tells whether the instruction has operand(s) or not.
hasPrevious() - Method in interface physis.core.iterator.DigitalOrganismIterator
Returns true if there is at least one organism before the current.
hasPrevious() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
hasPrevious() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
htxt - Variable in class physis.visualisation.panels.SpectrumIndicatorPanel
 

I

I - Static variable in class arche.UP
Instruction
id - Variable in class physis.core.task.TaskAdapter
 
id_generator - Static variable in class physis.core.task.TaskFactory
 
if_less - Static variable in class mar.virtualmachine.MarVM
 
if_n_equ - Static variable in class mar.virtualmachine.MarVM
 
if_n_equ() - Method in class mar.virtualmachine.MarVM
If the top of the stack is less than the registercontent executes the next instruction, otherwise skips it.
ifless() - Method in class mar.virtualmachine.MarVM
If the top of the stack is less than the registercontent executes the next instruction, otherwise skips it.
IFNOTZERO - Static variable in class arche.UP
 
ifnotzero(int) - Method in class arche.UP
Executes the next instruction if the content of thestructural element pointed by strel is zero.
IFZERO - Static variable in class arche.UP
 
ifzero(int) - Method in class arche.UP
Executes the next instruction if the content of thestructural element pointed by strel is zero.
in - Variable in class physis.core.DigitalOrganismProxy
 
in - Variable in class physis.core.RemoteDigitalOrganism
 
IN - Static variable in class arche.UP
 
in(int) - Method in class arche.UP
Reads one piece of data (an int) from the outside world (environment).
inc - Static variable in class mar.virtualmachine.MarVM
 
INC - Static variable in class arche.UP
 
inc() - Method in class mar.virtualmachine.MarVM
 
inc(int) - Method in class arche.UP
Increments the content of a structural element.
INC1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
INC2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
INC3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
INC4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
increaseAge() - Method in class physis.core.DigitalOrganismImpl
 
increaseAge() - Method in class physis.core.RemoteDigitalOrganism
 
increaseAge() - Method in interface physis.core.DigitalOrganism
Increments the age by 1.
increaseCounter() - Method in class physis.core.task.TaskAdapter
 
increaseCounter() - Method in interface physis.core.task.Task
If the task is performed, the counter should be increased.
increaseNumberOfBirths() - Method in class physis.core.genotype.GenomeData
 
increaseNumberOfSpawns() - Method in class physis.core.genotype.GenomeData
 
incrementIP(int) - Method in class mar.virtualmachine.MarVM
The instruction pointer-register is incremented.
incrementIP(int) - Method in class arche.UP
The instruction pointer-register is incremented.
index - Variable in class physis.core.RemoteDigitalOrganism
The index of the remote digital organism.
INFINITE_LOOP - Static variable in class physis.core.virtualmachine.PhysisVMTracer
The number of executed instructions which can be considered as inifinite loop.
init() - Static method in class physis.core.virtualmachine.GeneticCodeTapeFactory
 
init(String) - Static method in class physis.core.Configuration
 
initComponents() - Method in class physis.visualisation.PhysisGUI
 
initialize(StringTokenizer) - Method in class physis.core.triggers.TriggerImpl
Sets the type and the scheduling information according to the type.
initialize(StringTokenizer) - Method in interface physis.core.triggers.Trigger
Initializes the common parameters.
injectGenome(GeneticCodeTape) - Method in class physis.core.lifespace.MemoryPoolLifeSpace
 
injectGenome(GeneticCodeTape) - Method in class physis.core.lifespace.DistributedLattice2DLifeSpace
Injects the genome into the soup.
injectGenome(GeneticCodeTape) - Method in interface physis.core.lifespace.LifeSpace
Inserts a genome into the soup.
injectGenome(GeneticCodeTape) - Method in class physis.core.lifespace.Lattice2DLifeSpace
Injects the genome into the soup.
input_data_higher_bound - Variable in class physis.core.EnvironmentImpl
 
input_data_higher_bound - Variable in class physis.core.virtualmachine.PhysisVMTracer
 
INPUT_DATA_HIGHER_BOUND - Static variable in class physis.core.EnvironmentImpl
 
INPUT_DATA_HIGHER_BOUND - Static variable in class physis.core.virtualmachine.PhysisVMTracer
 
inputbuffer - Variable in class physis.core.Metabolism
 
insert_rate - Variable in class physis.core.EnvironmentImpl
 
INSERT_RATE - Static variable in class physis.core.EnvironmentImpl
 
insert() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
Inserts an instruction on a random position.
insert() - Method in interface physis.core.virtualmachine.GeneticCodeTape
Inserts an instruction on a random position.
insert() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Inserts an instruction on a random position.
inst_code - Variable in class physis.core.virtualmachine.Instruction
This is actually the main identifier of the instruction (the instruction itself).
instance - Static variable in class physis.core.virtualmachine.InstructionSet
 
instcodeArray - Variable in class physis.core.virtualmachine.InstructionSet
 
Instruction - class physis.core.virtualmachine.Instruction.
This class represents one instruction for a virtual machine.
INSTRUCTION - Static variable in class arche.UP
 
instruction_mnemonic - Variable in class physis.core.virtualmachine.Instruction
Actually it is the name of the instruction.
instruction_set - Static variable in class physis.core.DigitalOrganismProxy
 
instruction_set - Static variable in class physis.core.virtualmachine.SoupGeneticCodeTape
 
instruction_set - Static variable in class physis.core.virtualmachine.CellGeneticCodeTape
 
instruction_set - Static variable in class psoup.virtualmachine.PrimordialSoupVM
Reference for instruction set in order to access it quickly.
instruction_table - Variable in class arche.UP
 
Instruction(int, short, String, int) - Constructor for class physis.core.virtualmachine.Instruction
This class is immutable, which means that you can not change the state of an instance after you created.
InstructionPointer - class arche.InstructionPointer.
Queue as a structural element for processors.
InstructionPointer() - Constructor for class arche.InstructionPointer
 
instructions_by_codes - Variable in class physis.core.virtualmachine.InstructionSet
The keys are Integers, and the values are Instructions.
instructions_by_names - Variable in class physis.core.virtualmachine.InstructionSet
The keys are Strings (the names of the instructions), and the values are Instructions.
InstructionSet - class physis.core.virtualmachine.InstructionSet.
This class contains the instructons of an instructionset which belongs to one or more virtual machines.
InstructionSet(String) - Constructor for class physis.core.virtualmachine.InstructionSet
 
InteractionEvent - class physis.core.event.InteractionEvent.
When the virtual machine reads data from its environment, or writes data out this event is generated.
InteractionEvent(DigitalOrganism) - Constructor for class physis.core.event.InteractionEvent
 
InteractionEventListener - interface physis.core.event.InteractionEventListener.
Eventlistener for environment-organism interaction handling.
interactionOccured(InteractionEvent) - Method in class physis.core.EnvironmentImpl
 
interactionOccured(InteractionEvent) - Method in interface physis.core.event.InteractionEventListener
Performed when an organism interacts with its environment.
interactionOccured(InteractionEvent) - Method in class physis.core.virtualmachine.PhysisVMTracer
 
IP - Variable in class mar.virtualmachine.MarVM
instruction pointer
IP - Variable in class psoup.virtualmachine.PrimordialSoupVM
instruction pointer
IP - Variable in class arche.UP
 
iptr - Variable in class physis.core.Metabolism
The bufferpointers point to the last element.
is_cell - Static variable in class physis.core.virtualmachine.GeneticCodeTapeFactory
 
is_periodical - Variable in class physis.core.triggers.TriggerImpl
 
is_regionkill - Variable in class physis.core.triggers.DisasterTrigger
 
IS_SEP - Static variable in class arche.UP
 
is_sep(int, int) - Method in class arche.UP
 
isAlive - Variable in class physis.core.DigitalOrganismImpl
Indicates that the organism is ready to run
isAlive() - Method in class physis.core.DigitalOrganismImpl
 
isAlive() - Method in class physis.core.RemoteDigitalOrganism
 
isAlive() - Method in interface physis.core.DigitalOrganism
Tells whether the organism is alive or not.
isAllocated() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
isAllocated() - Method in interface physis.core.virtualmachine.GeneticCodeTape
Returns true if the cell already allocated space for the spawn.
isAllocated() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
 
isAllocationPossible(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
isAllocationPossible(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
The size must be in a predefined range, otherwise the allocation fails.
isAllocationPossible(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
 
isCodeForStructruralElement(short) - Method in class arche.UP
 
isCopied(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
isCopied(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Answers the question: is the positionth instruction copied?
isCopied(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
 
isEmpty() - Static method in class physis.core.genotype.GeneBank
 
isEmpty() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
isExecuted(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
isExecuted(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Answers the question: is the positionth instruction executed?
isExecuted(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
 
isExpired(int, long) - Method in class physis.core.genotype.GenomeData
This is used for deciding whether the genome should be removed or not.
isfertile - Variable in class physis.core.DigitalOrganismImpl
Indicates that the organism could bear at least one child
isFertile() - Method in class physis.core.DigitalOrganismImpl
 
isFertile() - Method in class physis.core.RemoteDigitalOrganism
 
isFertile() - Method in interface physis.core.DigitalOrganism
Tells whether the organism is fertile (capable to yield a child).
isFossil(int, long) - Method in class physis.core.genotype.GenomeData
When the genotype is inactive for a given period, than it is suppposed to be extinct.
isFull() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
isGeneBankEnabled() - Static method in class physis.core.Configuration
 
isInputFull() - Method in class physis.core.Metabolism
 
isMutated(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
isMutated(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Answers the question: is the positionth instruction mutated?
isMutated(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Answers the question: is the positionth instruction mutated?
isOutputFull() - Method in class physis.core.Metabolism
 
isProliferationPossible() - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
isProliferationPossible() - Method in interface physis.core.virtualmachine.GeneticCodeTape
Checks whether the organism is able to spawn (are there enough copied instructions?).
isProliferationPossible() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Checks whether the organism is able to spawn.
IT_DOESNT_COUNT_ANY_MORE - Static variable in class physis.core.DigitalOrganismImpl
When a task is performed too many times than it doesn't mean any bonus.
IT_DOESNT_COUNT_ANYMORE - Static variable in class physis.core.task.PerformedTasksRegister
 

J

JavaUtilRandom - class physis.core.random.JavaUtilRandom.
This is essentially the guts of java.util.Random as of jdk1.3.
JavaUtilRandom(long) - Constructor for class physis.core.random.JavaUtilRandom
 
JMPB - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
JMPF - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
JPZ1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
JPZ2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
JPZ3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
JPZ4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
JUMP - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
JUMP - Static variable in class arche.UP
 
jump_b - Static variable in class mar.virtualmachine.MarVM
 
jump_b() - Method in class mar.virtualmachine.MarVM
 
jump_f - Static variable in class mar.virtualmachine.MarVM
 
jump_f() - Method in class mar.virtualmachine.MarVM
 
jump(int) - Method in class arche.UP
Jumps to the address (mod codetape size).

K

KILL_TH - Static variable in class arche.UP
 
kill_th() - Method in class arche.UP
 
kill() - Method in class physis.core.DigitalOrganismImpl
Kills the organism.
kill() - Method in class physis.core.RemoteDigitalOrganism
Kills the organism.
kill() - Method in interface physis.core.DigitalOrganism
Kills the organism.

L

label_b - Static variable in class mar.virtualmachine.MarVM
 
label_f - Static variable in class mar.virtualmachine.MarVM
 
last_touched - Variable in class physis.core.genotype.GenomeData
The update number when last time something happened to this genotype.
Lattice2DLifeSpace - class physis.core.lifespace.Lattice2DLifeSpace.
dependency: Array2DDigitalOrganismIterator, ArrayDigitalOrganismIterator
Lattice2DLifeSpace() - Constructor for class physis.core.lifespace.Lattice2DLifeSpace
Creates a lifespace.
Lattice2DLifeSpace(int, int) - Constructor for class physis.core.lifespace.Lattice2DLifeSpace
Creates a lifespace with different with dimension x * y.
Lattice2DViewer - class physis.visualisation.panels.lifespace.Lattice2DViewer.
A panel which displays the whole lattice.
Lattice2DViewer() - Constructor for class physis.visualisation.panels.lifespace.Lattice2DViewer
 
LBL0 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL5 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL6 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL7 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL8 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
LBL9 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
lifespace - Variable in class physis.core.Population
 
lifespace - Variable in class physis.core.EnvironmentImpl
 
lifespace - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
lifespace - Variable in class physis.core.lifespace.Lattice2DLifeSpace
 
LifeSpace - interface physis.core.lifespace.LifeSpace.
LifeSpace is the space where the digital organisms live.
LIFESPACE_CLASS_NAME - Static variable in class physis.core.lifespace.LifeSpaceFactory
 
LifeSpaceFactory - class physis.core.lifespace.LifeSpaceFactory.
 
LifeSpaceFactory() - Constructor for class physis.core.lifespace.LifeSpaceFactory
 
LifeSpaceViewer - interface physis.visualisation.panels.lifespace.LifeSpaceViewer.
Interface for viewers which display lifespaces.
LOAD - Static variable in class arche.UP
 
load(int, int) - Method in class arche.UP
Loads data from memory pointed by the source structural element.
loadCodeTape(GeneticCodeTape) - Method in class physis.core.virtualmachine.PhysisVirtualMachine
Loads the codetape into the VM.
loadTriggers(String) - Method in class physis.core.triggers.Triggers
 
loc - Variable in class physis.core.virtualmachine.SoupGeneticCodeTape
The location of this codetape in the big pool.
LOCALEAST - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
LocalLandscapeAnalyzer - class physis.core.genotype.LocalLandscapeAnalyzer.
Wtih this class a given genotype's neighbouring genotypes can be generated and analyzed.
LocalLandscapeAnalyzer() - Constructor for class physis.core.genotype.LocalLandscapeAnalyzer
 
LOCALNORTH - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
localRef - Variable in class physis.core.RemoteDigitalOrganism
If the connection breaks down this local reference shoud be used.
LOCALSOUTH - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
LOCALWEST - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
Log - class physis.log.Log.
This is a general tool which makes the logging easier.
Log() - Constructor for class physis.log.Log
 
LOWER_MASK - Static variable in class physis.core.random.MersenneTwister
 
lsviewer - Variable in class physis.visualisation.PhysisGUI
 
ltxt - Variable in class physis.visualisation.panels.SpectrumIndicatorPanel
 

M

M - Static variable in class physis.core.random.MersenneTwister
 
M1R2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
M1R3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
M1R4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
M2R1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
M2R3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
M2R4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
mag01 - Variable in class physis.core.random.MersenneTwister
 
main(String[]) - Static method in class physis.core.PHYSIS
This is the main entry point.
main(String[]) - Static method in class physis.core.random.JavaUtilRandom
 
main(String[]) - Static method in class physis.core.random.MersenneTwister
Tests the code.
main(String[]) - Static method in class physis.core.virtualmachine.PhysisVMTracer
 
main(String[]) - Static method in class physis.log.Log
 
main(String[]) - Static method in class physis.visualisation.PhysisGUI
 
mar.virtualmachine - package mar.virtualmachine
 
MarVM - class mar.virtualmachine.MarVM.
Simple stack machine with one stack and one register.
MarVM() - Constructor for class mar.virtualmachine.MarVM
 
mask - Static variable in class physis.core.random.JavaUtilRandom
 
MATRIX_A - Static variable in class physis.core.random.MersenneTwister
 
max_age - Variable in class physis.core.Population
 
MAX_AGE - Static variable in class physis.core.triggers.OrganismExtractTrigger
 
max_age_ever_reached - Variable in class physis.core.Population
 
max_age_org - Variable in class physis.core.Population
 
max_allocation_ratio - Static variable in class physis.core.Configuration
When a digital organism tries to allocate space for its child it's only allowed to do it if the size of the allocated area is smaller than original_size * max_allocation_ratio.
MAX_ALLOCATION_RATIO - Static variable in class physis.core.Configuration
 
MAX_COMM - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
max_effective_length - Variable in class physis.core.Population
 
max_effective_length_ever_reached - Variable in class physis.core.Population
 
max_elength_org - Variable in class physis.core.Population
 
max_fitness - Variable in class physis.core.Population
 
MAX_FITNESS - Static variable in class physis.core.triggers.OrganismExtractTrigger
 
max_fitness_ever_reached - Variable in class physis.core.Population
 
max_fitness_org - Variable in class physis.core.Population
 
max_genome_length - Variable in class physis.core.Population
 
max_genome_length_ever_reached - Variable in class physis.core.Population
 
max_glength_org - Variable in class physis.core.Population
 
max_merit - Variable in class physis.core.Population
 
MAX_MERIT - Static variable in class physis.core.triggers.OrganismExtractTrigger
 
max_merit_ever_reached - Variable in class physis.core.Population
 
max_merit_org - Variable in class physis.core.Population
 
max_number_of_tasks - Static variable in class physis.core.Configuration
If it's less than the actual loaded tasks then it may be reset by TaskLibrary.
MAX_NUMBER_OF_TASKS - Static variable in class physis.core.Configuration
 
MAX_NUMBER_OF_UPDATES - Static variable in class physis.core.Configuration
 
max_size - Variable in class arche.StorageArray
 
max_task_size - Static variable in class physis.core.Configuration
It comes from when building the tasklibrary.
max_updates - Variable in class physis.core.PHYSIS
The maximum number of possible updates is defined in the configuration file.
MaxAgePerMeritNurse - class physis.core.nursing.MaxAgePerMeritNurse.
A Nurse which favors organisms with high merit and they're not too old.
MaxAgePerMeritNurse() - Constructor for class physis.core.nursing.MaxAgePerMeritNurse
 
MAXER_COMM - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
maximum_number_of_updates - Static variable in class physis.core.Configuration
The maximum number of updates that the system is allowed to perform.
memory - Variable in class physis.core.virtualmachine.CellGeneticCodeTape
The instructions are represented with a thin class called InstructionCode.
MemoryPoolLifeSpace - class physis.core.lifespace.MemoryPoolLifeSpace.
 
MemoryPoolLifeSpace() - Constructor for class physis.core.lifespace.MemoryPoolLifeSpace
 
merit - Variable in class physis.core.DigitalOrganismImpl
The organism's merit
Merit - class physis.core.Merit.
It's the merit of the digital organism.
MERIT - Static variable in class physis.core.DigitalOrganismProxy
 
MERIT - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
MERIT_COMM - Static variable in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
Merit() - Constructor for class physis.core.Merit
 
merit(int) - Method in class physis.core.DigitalOrganismProxy
Writes to the socket the organism's fitness.
meritmultipliers - Variable in class physis.core.task.TaskAdapter
 
MeritScheduler - class physis.core.scheduler.MeritScheduler.
Another dummy scheduler.
MeritScheduler() - Constructor for class physis.core.scheduler.MeritScheduler
 
MersenneTwister - class physis.core.random.MersenneTwister.
Mersenne Twister
MersenneTwister() - Constructor for class physis.core.random.MersenneTwister
Constructor using the default seed.
MersenneTwister(long) - Constructor for class physis.core.random.MersenneTwister
Constructor using a given seed.
metabolism - Variable in class physis.core.DigitalOrganismImpl
It is actually the virtualmachine's I/O buffer.
Metabolism - class physis.core.Metabolism.
It tracks the organism's interaction with the environment.
Metabolism(int) - Constructor for class physis.core.Metabolism
 
min_allocation_ratio - Static variable in class physis.core.Configuration
When a digital organism tries to allocate space for its child it's only allowed to do it if the size of the allocated area is bigger than original_size * min_allocation_ratio.
MIN_ALLOCATION_RATIO - Static variable in class physis.core.Configuration
 
min_fitness - Variable in class physis.core.Population
 
min_merit - Variable in class physis.core.Population
 
min_proliferation_ratio - Static variable in class physis.core.Configuration
 
MIN_PROLIFERATION_RATIO - Static variable in class physis.core.Configuration
 
MOD - Static variable in class arche.UP
 
mod(int, int, int) - Method in class arche.UP
 
MOVE - Static variable in class arche.UP
 
move(int, int) - Method in class arche.UP
Moves data between the SEs.
mt - Variable in class physis.core.random.MersenneTwister
 
mti - Variable in class physis.core.random.MersenneTwister
 
MUL - Static variable in class arche.UP
 
mul(int, int, int) - Method in class arche.UP
 
multiplier - Static variable in class physis.core.random.JavaUtilRandom
 
multiplyBonus(double) - Method in class physis.core.Merit
Multiplies bonus multiplier.
mutate(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
mutate(int) - Method in interface physis.core.virtualmachine.GeneticCodeTape
Mutate the specified instruction.
mutate(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Mutate the specified instruction.
MUTATED - Static variable in interface physis.core.virtualmachine.GeneticCodeTape
Instruction-attribute: the instruction was mutated.

N

N - Static variable in class physis.core.random.MersenneTwister
 
name - Variable in class physis.core.genotype.GenomeData
The name of the genome: _ e.g.: 72_bAe
name - Variable in class physis.core.task.TaskGroup
 
name - Variable in class physis.core.virtualmachine.InstructionSet
The identifier name of the instructionset.
nand - Static variable in class mar.virtualmachine.MarVM
 
nand() - Method in class mar.virtualmachine.MarVM
 
NEG - Static variable in class arche.UP
 
neg(int, int) - Method in class arche.UP
 
neighbour - Variable in class physis.core.DigitalOrganismImpl
One of the organism's neighbours is special because all the close interactions happen between two organism.
neighbour_iterator - Variable in class physis.core.lifespace.MemoryPoolLifeSpace
 
neighbour_iterator - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
neighbour_iterator - Variable in class physis.core.lifespace.Lattice2DLifeSpace
 
neighbours - Variable in class physis.core.lifespace.MemoryPoolLifeSpace
 
neighbours - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
neighbours - Variable in class physis.core.lifespace.Lattice2DLifeSpace
 
NEIGHBOURS - Static variable in class physis.core.lifespace.MemoryPoolLifeSpace
 
newSeed - Variable in class physis.core.event.ProliferationEvent
The new codetape.
next - Variable in class physis.core.triggers.TriggerImpl
The update number of the next time when it should run.
next() - Method in interface physis.core.iterator.DigitalOrganismIterator
Returns the next DigitalOrganism from this collection.
next() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
next() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
next() - Method in class physis.core.task.TaskIterator
 
next(int) - Method in class physis.core.random.Randomness
To extend this class, all you need to do is implement this method!
next(int) - Method in class physis.core.random.JavaUtilRandom
Generates the next pseudorandom number.
next(int) - Method in class physis.core.random.MersenneTwister
Returns an integer with bits bits filled with a random number.
nextBoolean() - Method in class physis.core.random.Randomness
 
nextBoolean(double) - Method in class physis.core.random.Randomness
This generates a coin flip with a probability probability of returning true, else returning false.
nextByte() - Method in class physis.core.random.Randomness
 
nextBytes(byte[]) - Method in class physis.core.random.Randomness
A bug fix for all versions of the JDK.
nextDouble() - Method in class physis.core.random.Randomness
 
nextFloat() - Method in class physis.core.random.Randomness
 
nextInt() - Method in class physis.core.random.Randomness
Returns a 32 bit uniformly distributed random number in the closed interval [Integer.MIN_VALUE,Integer.MAX_VALUE] (including Integer.MIN_VALUE and Integer.MAX_VALUE).
nextInt(int) - Method in class physis.core.random.Randomness
 
nextLong() - Method in class physis.core.random.Randomness
Returns a 64 bit uniformly distributed random number in the closed interval [Long.MIN_VALUE,Long.MAX_VALUE] (including Long.MIN_VALUE and Long.MAX_VALUE).
nf - Variable in class physis.core.statistics.StatisticsImpl
 
nf_s - Variable in class physis.core.statistics.StatisticsImpl
 
nfo - Variable in class physis.core.statistics.StatisticsImpl
 
nfo_s - Variable in class physis.core.statistics.StatisticsImpl
 
nlo - Variable in class physis.core.statistics.StatisticsImpl
 
nlo_s - Variable in class physis.core.statistics.StatisticsImpl
 
nm - Variable in class physis.core.statistics.StatisticsImpl
 
nm_s - Variable in class physis.core.statistics.StatisticsImpl
 
NNR1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
NNR2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
NNR3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
NNR4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
NOOP - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
nop - Static variable in class mar.virtualmachine.MarVM
 
NOP - Static variable in class arche.UP
 
north - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
NORTH - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
north_server - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
NOT - Static variable in class arche.UP
 
not(int, int) - Method in class arche.UP
 
number_of_allocated_regs - Variable in class arche.StorageArray
 
number_of_births - Variable in class physis.core.genotype.GenomeData
 
number_of_fertile_organisms - Variable in class physis.core.Population
 
number_of_living_organisms - Variable in class physis.core.Population
 
number_of_occurence - Variable in class physis.core.genotype.GeneticSnapshot.Data
 
number_of_operands - Variable in class physis.core.virtualmachine.Instruction
The number of operands.
number_of_spawns - Variable in class physis.core.genotype.GenomeData
 
nurse - Variable in class physis.core.EnvironmentImpl
 
Nurse - interface physis.core.nursing.Nurse.
A new digital organism has to be placed somewhere in the lifespace.
NURSE_CLASS_NAME - Static variable in class physis.core.Configuration
 
NurseFactory - class physis.core.nursing.NurseFactory.
Creates a Nurse.
NurseFactory() - Constructor for class physis.core.nursing.NurseFactory
 

O

OldestNurse - class physis.core.nursing.OldestNurse.
A Nurse which kills the oldest organism in the neighbourhood if there's no empty cell.
OldestNurse() - Constructor for class physis.core.nursing.OldestNurse
 
operands - Variable in class arche.UP
puffer for operands - 3 is the maximum number of operands
optr - Variable in class physis.core.Metabolism
 
OR - Static variable in class arche.UP
 
or(int, int, int) - Method in class arche.UP
 
org - Variable in class physis.core.virtualmachine.PhysisVMTracer
 
organism - Variable in class physis.core.event.BiologicalEvent
This is the source of the event.
OrganismExtractTrigger - class physis.core.triggers.OrganismExtractTrigger.
 
OrganismExtractTrigger() - Constructor for class physis.core.triggers.OrganismExtractTrigger
 
orgs - Variable in class physis.core.DigitalOrganismProxy
 
orgs - Variable in class physis.core.genotype.GeneticSnapshot
 
orgs - Variable in class physis.core.iterator.Array2DDigitalOrganismIterator
 
orgs - Variable in class physis.core.iterator.ArrayDigitalOrganismIterator
 
orgs - Variable in class physis.core.lifespace.MemoryPoolLifeSpace
 
orgs - Variable in class physis.core.scheduler.ConstantScheduler
 
orgs - Variable in class physis.core.scheduler.MeritScheduler
 
orgs - Variable in class physis.core.scheduler.ScaledMeritScheduler
 
orig - Variable in class physis.core.virtualmachine.PhysisVMTracer
 
out - Variable in class physis.core.DigitalOrganismProxy
 
out - Variable in class physis.core.RemoteDigitalOrganism
 
OUT - Static variable in class arche.UP
 
out(int) - Method in class arche.UP
Writes one piece of data (an int) to the outside world (environment).
OUTPUT_FILE - Static variable in class physis.core.genotype.GeneBank
 
outputbuffer - Variable in class physis.core.Metabolism
 

P

p1 - Variable in class arche.Queue
The pointers.
p2 - Variable in class arche.Queue
The pointers.
paint(Graphics) - Method in class physis.visualisation.panels.ColorRangePanel
 
paint(Graphics) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
ParallelScheduler - class physis.core.scheduler.ParallelScheduler.
This method implements the possibly best parallel scheduling.
ParallelScheduler() - Constructor for class physis.core.scheduler.ParallelScheduler
 
ParallelVirtualMachine - class physis.core.virtualmachine.ParallelVirtualMachine.
This VM can run multiple threads concurrently.
ParallelVirtualMachine() - Constructor for class physis.core.virtualmachine.ParallelVirtualMachine
 
ParameterTrigger - class physis.core.triggers.ParameterTrigger.
A parametertrigger can adjust the system-parameters in the Configuration class.
ParameterTrigger() - Constructor for class physis.core.triggers.ParameterTrigger
 
parent - Variable in class physis.core.genotype.GenomeData
The reference to the parent genome.
PCR1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
PCR2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
PCR3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
PCR4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
percent - Variable in class physis.core.triggers.ChangeTaskBonusesTrigger
 
percentage - Variable in class physis.core.triggers.DisasterTrigger
 
performed_tasks - Variable in class physis.core.DigitalOrganismImpl
This hashtable keeps track the performed tasks.
PerformedTasksRegister - class physis.core.task.PerformedTasksRegister.
 
PerformedTasksRegister(int) - Constructor for class physis.core.task.PerformedTasksRegister
 
physis - Static variable in class physis.core.PHYSIS
The instance of the system.
physis - Static variable in class physis.core.genotype.GeneBank
 
physis - Static variable in class physis.visualisation.PhysisGUI
 
PHYSIS - class physis.core.PHYSIS.
This is the main starter class.
physis_home - Static variable in class physis.core.Configuration
 
PHYSIS_HOME - Static variable in class physis.core.Configuration
 
physis.core - package physis.core
 
physis.core.event - package physis.core.event
 
physis.core.genotype - package physis.core.genotype
 
physis.core.iterator - package physis.core.iterator
Specialized iterators for performance reasons.
physis.core.lifespace - package physis.core.lifespace
The abstraction of the lifespace (topology, memory-model, accessing different subsets of organisms).
physis.core.nursing - package physis.core.nursing
 
physis.core.random - package physis.core.random
A pluggable architecture for using different random number generators.
physis.core.scheduler - package physis.core.scheduler
 
physis.core.statistics - package physis.core.statistics
 
physis.core.task - package physis.core.task
 
physis.core.task.advanced - package physis.core.task.advanced
 
physis.core.task.basic - package physis.core.task.basic
 
physis.core.task.math - package physis.core.task.math
 
physis.core.triggers - package physis.core.triggers
 
physis.core.virtualmachine - package physis.core.virtualmachine
Contains the base classes for software implementations of processors.
physis.log - package physis.log
 
physis.visualisation - package physis.visualisation
The root of the packages for visualisation and GUI system.
physis.visualisation.panels - package physis.visualisation.panels
 
physis.visualisation.panels.lifespace - package physis.visualisation.panels.lifespace
 
physis.visualisation.util - package physis.visualisation.util
 
PHYSIS(String) - Constructor for class physis.core.PHYSIS
 
PhysisGUI - class physis.visualisation.PhysisGUI.
The main window and an alternative entry point to the system.
PhysisGUI() - Constructor for class physis.visualisation.PhysisGUI
 
PhysisVirtualMachine - class physis.core.virtualmachine.PhysisVirtualMachine.
This is the base class for all virtualmachines which are implemented in Physis.
PhysisVirtualMachine() - Constructor for class physis.core.virtualmachine.PhysisVirtualMachine
 
PhysisVMTracer - class physis.core.virtualmachine.PhysisVMTracer.
A separate tool for running one virtualmachine.
PhysisVMTracer() - Constructor for class physis.core.virtualmachine.PhysisVMTracer
 
placeNewBorn(GeneticCodeTape, DigitalOrganismIterator, int) - Method in class physis.core.nursing.MaxAgePerMeritNurse
A new organism should be placed somewhere in the parent's neighbourhood.
placeNewBorn(GeneticCodeTape, DigitalOrganismIterator, int) - Method in interface physis.core.nursing.Nurse
A new organism should be placed somewhere in the parent's neighbourhood.
placeNewBorn(GeneticCodeTape, DigitalOrganismIterator, int) - Method in class physis.core.nursing.OldestNurse
A new organism should be placed somewhere in the parent's neighbourhood.
pool - Static variable in class physis.core.virtualmachine.SoupGeneticCodeTape
This is the big memory pool.
POOL_SIZE - Static variable in class physis.core.virtualmachine.GeneticCodeTapeFactory
 
pop - Static variable in class mar.virtualmachine.MarVM
 
pop - Variable in class physis.core.statistics.StatisticsImpl
 
pop() - Method in class mar.virtualmachine.MarVM
 
pop() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
POP1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
POP2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
POP3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
POP4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
population - Variable in class physis.core.PHYSIS
There's one population in one instance of Physis.
population - Variable in class physis.core.triggers.DataExtractTrigger
Extraact-triggers should access the population, that's why they have the reference.
population - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
Population - class physis.core.Population.
Population class represents the whole population running in one concrete instance of the system.
Population() - Constructor for class physis.core.Population
 
position_info - Variable in class physis.core.DigitalOrganismImpl
This is information about the position of the organism in the lifespace.
PositionInfo2DLattice - class physis.core.lifespace.PositionInfo2DLattice.
 
PositionInfo2DLattice(int, int) - Constructor for class physis.core.lifespace.PositionInfo2DLattice
 
prev_seq - Static variable in class physis.core.genotype.GeneBank
 
previous() - Method in interface physis.core.iterator.DigitalOrganismIterator
Returns the previous DigitalOrganism from this collection.
previous() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
previous() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
primes - Static variable in class physis.core.genotype.Genome
 
PrimordialSoupVM - class psoup.virtualmachine.PrimordialSoupVM.
 
PrimordialSoupVM() - Constructor for class psoup.virtualmachine.PrimordialSoupVM
 
printAsText() - Static method in class physis.core.genotype.GeneBank
 
printHeader() - Method in class physis.core.statistics.StatisticsImpl
 
printMemoryInfo() - Static method in class physis.log.Log
 
processActualTriggers(long) - Method in class physis.core.triggers.Triggers
Checks the triggers in the container if they have the propper updatecount to activate.
processSettings(Properties) - Method in class physis.core.statistics.StatisticsImpl
 
ProliferationEvent - class physis.core.event.ProliferationEvent.
When an organism divides this event is generated.
ProliferationEvent(GeneticCodeTape, DigitalOrganism) - Constructor for class physis.core.event.ProliferationEvent
 
ProliferationEventListener - interface physis.core.event.ProliferationEventListener.
 
proliferationPerformed(ProliferationEvent) - Method in class physis.core.EnvironmentImpl
 
proliferationPerformed(ProliferationEvent) - Method in interface physis.core.event.ProliferationEventListener
When a digital organism divides the new organism must be placed somewhere in the lifespace and the old organism's effective length should be recalculated.
proliferationPerformed(ProliferationEvent) - Method in class physis.core.virtualmachine.PhysisVMTracer
 
props - Static variable in class physis.core.Configuration
 
PSH1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
PSH2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
PSH3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
PSH4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
PSHP - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
psoup.virtualmachine - package psoup.virtualmachine
 
push - Static variable in class mar.virtualmachine.MarVM
 
push() - Method in class mar.virtualmachine.MarVM
 
push(int) - Method in class psoup.virtualmachine.PrimordialSoupVM
 
put - Static variable in class mar.virtualmachine.MarVM
 
Put - class physis.core.task.basic.Put.
 
put() - Method in class mar.virtualmachine.MarVM
 
Put() - Constructor for class physis.core.task.basic.Put
 
putInputValue(int) - Method in class physis.core.Metabolism
Put a value into the input queue.
putOutputValue(int) - Method in class physis.core.Metabolism
Put a value into the output queue.

Q

Q - Static variable in class arche.UP
Queue
queue - Variable in class arche.Queue
 
Queue - class arche.Queue.
Queue as a structural element for processors.
Queue(int) - Constructor for class arche.Queue
 

R

R - Static variable in class arche.UP
Register.
R1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R1M2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R1R2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R1R3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R1R4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R2M1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R2R1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R3M1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R3M2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R3R1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R4M1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R4M2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
R4R1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
random - Variable in class physis.core.virtualmachine.InstructionSet
 
RANDOM_SEED - Static variable in class physis.core.EnvironmentImpl
 
randomly() - Method in interface physis.core.iterator.DigitalOrganismIterator
Returns one organism from the underlying collection.
randomly() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
randomly() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
Randomness - class physis.core.random.Randomness.
class Randomness - a very plain boring name for basically a random number generator abstraction layer.
Randomness(long) - Constructor for class physis.core.random.Randomness
 
raw() - Method in class physis.core.random.Randomness
Returns a 32 bit uniformly distributed random number in the open unit interval (0.0,1.0) (excluding 0.0 and 1.0).
read() - Method in class arche.Storage
 
read() - Method in class arche.Stack
 
read() - Method in class arche.Register
Returns the value stored in this register.
read() - Method in class arche.Queue
 
read(int) - Method in interface physis.core.virtualmachine.CodeTape
Returns the instruction on a given position of the tape.
read(int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
It gives the instruction on the specified position.
read(int) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
It gives the instruction on the specified position.
recalculateBonus(double) - Method in class physis.core.DigitalOrganismImpl
 
recalculateBonus(double) - Method in class physis.core.RemoteDigitalOrganism
 
recalculateBonus(double) - Method in interface physis.core.DigitalOrganism
Recalculates the organism's bonus by multiplying it with the bonus multiplier.
recalculateEffectiveLength() - Method in class physis.core.DigitalOrganismImpl
 
recalculateEffectiveLength() - Method in class physis.core.RemoteDigitalOrganism
 
recalculateEffectiveLength() - Method in interface physis.core.DigitalOrganism
Recalculates the effective length.
recalculateFitness() - Method in class physis.core.DigitalOrganismImpl
 
recalculateFitness() - Method in class physis.core.RemoteDigitalOrganism
 
recalculateFitness() - Method in interface physis.core.DigitalOrganism
Recalculates the fitness.
receive(int) - Method in class arche.UP
Receives a piece of data from an other processor.
RECIEVE - Static variable in class arche.UP
 
refresh() - Method in interface physis.visualisation.Viewer
This method refreshes the viewer's state according to the changes in the population.
refresh() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
Refreshes the viewer's internal data about the population.
refreshAge() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
refreshFitness() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
refreshMerit() - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
refreshSpectrumIndicator(String, double, double) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
reg - Variable in class arche.Register
For stroing the value.
register - Variable in class mar.virtualmachine.MarVM
 
Register - class arche.Register.
Simple one-value register as a basic storage for processors.
Register() - Constructor for class arche.Register
 
register(Genome, Genome) - Static method in class physis.core.genotype.GeneBank
 
REL_LOAD - Static variable in class arche.UP
 
rel_load(int, int, int) - Method in class arche.UP
 
REL_STORE - Static variable in class arche.UP
 
rel_store(int, int, int) - Method in class arche.UP
 
Remote2DLattice - interface physis.core.lifespace.Remote2DLattice.
Remote interface for distributed two-dimensional lattice.
RemoteDigitalOrganism - class physis.core.RemoteDigitalOrganism.
This class represents a remote digital organism.
RemoteDigitalOrganism(int, Socket, BufferedReader, PrintWriter, DigitalOrganism) - Constructor for class physis.core.RemoteDigitalOrganism
 
removeTrigger(int) - Method in class physis.core.triggers.Triggers
Removes a trigger from the indexth position.
reset() - Method in class mar.virtualmachine.MarVM
Brings the machine into the base-state.
reset() - Method in interface physis.core.iterator.DigitalOrganismIterator
Resets the iterator: the enumerating of organisms can be repeated from the begining..
reset() - Method in class physis.core.iterator.Array2DDigitalOrganismIterator
 
reset() - Method in class physis.core.iterator.ArrayDigitalOrganismIterator
 
reset() - Method in class physis.core.task.TaskIterator
 
reset() - Method in class physis.core.virtualmachine.VirtualMachine
Resets the virtual machine's state.
reset() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
reset() - Method in class arche.UP
 
restart() - Method in class mar.virtualmachine.MarVM
Brings the machine into base-state but doesn't change the gestation time.
restart() - Method in class physis.core.virtualmachine.PhysisVirtualMachine
This should be called after successfull proliferation.
restart() - Method in class psoup.virtualmachine.PrimordialSoupVM
 
restart() - Method in class arche.UP
 
RETN - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
Reverse - class physis.core.task.advanced.Reverse.
 
Reverse() - Constructor for class physis.core.task.advanced.Reverse
 
rnd - Variable in class physis.core.EnvironmentImpl
 
rnd - Variable in class physis.core.lifespace.MemoryPoolLifeSpace
 
rnd - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
rnd - Variable in class physis.core.lifespace.Lattice2DLifeSpace
 
rnd - Variable in class physis.core.virtualmachine.PhysisVMTracer
 
rotate_b - Static variable in class mar.virtualmachine.MarVM
 
rotate_b() - Method in class mar.virtualmachine.MarVM
 
rotate_f - Static variable in class mar.virtualmachine.MarVM
 
rotate_f() - Method in class mar.virtualmachine.MarVM
 
rotate_rand - Static variable in class mar.virtualmachine.MarVM
 
rotate_rand() - Method in class mar.virtualmachine.MarVM
 
rotateForward(DigitalOrganism) - Method in class physis.core.EnvironmentImpl
Rotates the organism's facing forward.
rotateForward(DigitalOrganism) - Method in interface physis.core.Environment
 
rotateForward(DigitalOrganism) - Method in class physis.core.virtualmachine.PhysisVMTracer
Rotates the organism's facing forward.
run() - Method in class physis.core.DigitalOrganismProxy
 
run() - Method in class physis.core.PHYSIS
The thread's run method.

S

S - Static variable in class arche.UP
Stack
sample_rate - Variable in class physis.core.statistics.StatisticsImpl
 
SAMPLE_RATE - Variable in class physis.core.statistics.StatisticsImpl
 
ScaledMeritScheduler - class physis.core.scheduler.ScaledMeritScheduler.
A somewhat more sophisticated scheduler.
ScaledMeritScheduler() - Constructor for class physis.core.scheduler.ScaledMeritScheduler
 
SCB1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SCB2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SCB3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SCB4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SCF1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SCF2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SCF3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SCF4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
scheduler - Variable in class physis.core.Population
 
Scheduler - interface physis.core.scheduler.Scheduler.
The digital organisms live together in the same space and in the same time.
SCHEDULER_CLASS_NAME - Static variable in class physis.core.scheduler.SchedulerFactory
 
SchedulerFactory - class physis.core.scheduler.SchedulerFactory.
 
SchedulerFactory() - Constructor for class physis.core.scheduler.SchedulerFactory
 
scheduleUpdate(int) - Method in class physis.core.scheduler.ParallelScheduler
 
scheduleUpdate(int) - Method in class physis.core.scheduler.ConstantScheduler
 
scheduleUpdate(int) - Method in class physis.core.scheduler.MeritScheduler
 
scheduleUpdate(int) - Method in interface physis.core.scheduler.Scheduler
It schedules the executing of each digital organisms.
scheduleUpdate(int) - Method in class physis.core.scheduler.ScaledMeritScheduler
 
SDIR - Static variable in class arche.UP
 
sdir(int) - Method in class arche.UP
Th processor can communicate with other processors in its neighbourhood but only with one in a moment.
searchBackward(int, short, int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
searchForDominant() - Method in class physis.core.genotype.GeneticSnapshot
 
searchForward(int, short, int) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
seed - Variable in class physis.core.random.JavaUtilRandom
 
SEED_ORGANISM - Static variable in class physis.core.Population
 
SEND - Static variable in class arche.UP
 
send(int) - Method in class arche.UP
Sends a piece of data to an other processor pointed by the direction.
SEPARATOR - Static variable in class arche.UP
Separator
separator_position - Variable in class arche.UP
 
server - Variable in class physis.core.DigitalOrganismProxy
 
ses - Variable in class arche.UP
The structural elements.
setAverageTimeSlice(int) - Static method in class physis.core.Configuration
 
setBearer(DigitalOrganism) - Method in class physis.core.virtualmachine.PhysisVirtualMachine
Sets the bearer organism of the VM.
setBonusMultiplier(double) - Method in class physis.core.Merit
Sets the bonus multiplier.
setCellSize(int) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
setColorAssignmentMode(int) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
setColorRange(ColorRange) - Method in class physis.visualisation.panels.ColorRangePanel
 
setColorRangeSize(int) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
setConfigFileName(String) - Static method in class physis.core.PHYSIS
Sets the configuration file.
setEffectiveLength(int) - Method in class physis.core.Merit
Sets the effective length.
setFertile(boolean) - Method in class physis.core.DigitalOrganismImpl
 
setFertile(boolean) - Method in class physis.core.RemoteDigitalOrganism
 
setFertile(boolean) - Method in interface physis.core.DigitalOrganism
Sets the fertility flag.
setGeneBankEnabled(boolean) - Static method in class physis.core.Configuration
 
setGeneBankMaxSize(int) - Static method in class physis.core.Configuration
 
setHigh(double) - Method in class physis.visualisation.panels.SpectrumIndicatorPanel
 
setID(int) - Method in class physis.core.task.TaskAdapter
 
setID(int) - Method in interface physis.core.task.Task
Sets the internal ID
setIP(int) - Method in class mar.virtualmachine.MarVM
 
setIP(int) - Method in class psoup.virtualmachine.PrimordialSoupVM
Just sets directly the IP.
setIP(int) - Method in class arche.UP
Directly sets the instruction pointer.
setLastTouch(long) - Method in class physis.core.genotype.GenomeData
 
setLifeSpace(LifeSpace) - Method in class physis.core.EnvironmentImpl
 
setLifeSpace(LifeSpace) - Method in interface physis.core.Environment
 
setLifeSpace(LifeSpace) - Method in class physis.core.virtualmachine.PhysisVMTracer
 
setLow(double) - Method in class physis.visualisation.panels.SpectrumIndicatorPanel
 
setMaxAllocationRatio(double) - Static method in class physis.core.Configuration
 
setMaxNumberOfTasks(int) - Static method in class physis.core.Configuration
 
setMaxNumberOfUpdates(long) - Static method in class physis.core.Configuration
 
setMaxTaskSize(int) - Static method in class physis.core.Configuration
 
setMeritMultipliers(double[]) - Method in class physis.core.task.TaskAdapter
 
setMeritMultipliers(double[]) - Method in interface physis.core.task.Task
Sets the meritmultipliers.
setMinAllocationRatio(double) - Static method in class physis.core.Configuration
 
setMinProliferationRatio(double) - Static method in class physis.core.Configuration
 
setName(String) - Method in class physis.core.genotype.GenomeData
 
setNeighbour(DigitalOrganism) - Method in class physis.core.DigitalOrganismImpl
 
setNeighbour(DigitalOrganism) - Method in class physis.core.RemoteDigitalOrganism
 
setNeighbour(DigitalOrganism) - Method in interface physis.core.DigitalOrganism
Sets the organism neighbour.
setParameters(StringTokenizer) - Method in class physis.core.triggers.TriggerImpl
Should be overridden in implementations.
setParameters(StringTokenizer) - Method in class physis.core.triggers.OrganismExtractTrigger
 
setParameters(StringTokenizer) - Method in class physis.core.triggers.ChangeTaskBonusesTrigger
 
setParameters(StringTokenizer) - Method in class physis.core.triggers.DisasterTrigger
 
setParameters(StringTokenizer) - Method in interface physis.core.triggers.Trigger
The specific initialization parameters are in a string separated by whitespaces.
setParameters(StringTokenizer) - Method in class physis.core.triggers.GeneticSnapshotTrigger
 
setPhysisHome(String) - Static method in class physis.core.Configuration
 
setPositionInfo(Object) - Method in class physis.core.DigitalOrganismImpl
 
setPositionInfo(Object) - Method in class physis.core.RemoteDigitalOrganism
 
setPositionInfo(Object) - Method in interface physis.core.DigitalOrganism
Sets the position information.
setSeed(long) - Method in class physis.core.random.JavaUtilRandom
 
setSeed(long) - Method in class physis.core.random.MersenneTwister
Initalize the pseudo random number generator.
setSeedOld(long) - Method in class physis.core.random.MersenneTwister
Initalize the pseudo random number generator.
setSpectrum(ColorRange) - Method in class physis.visualisation.panels.SpectrumIndicatorPanel
 
setSpectrumIndicator(SpectrumIndicatorPanel) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
setSpectrumIndicator(SpectrumIndicatorPanel) - Method in interface physis.visualisation.panels.lifespace.LifeSpaceViewer
 
setTitle(String) - Method in class physis.visualisation.panels.SpectrumIndicatorPanel
 
setViewers(Viewer[]) - Method in class physis.core.PHYSIS
The viewers can be set dynamically.
setViewMode(int) - Method in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
setVMClassName(String) - Static method in class physis.core.Configuration
 
shift_l - Static variable in class mar.virtualmachine.MarVM
 
SHIFT_L - Static variable in class arche.UP
 
shift_l() - Method in class mar.virtualmachine.MarVM
 
shift_l(int, int) - Method in class arche.UP
 
shift_r - Static variable in class mar.virtualmachine.MarVM
 
SHIFT_R - Static variable in class arche.UP
 
shift_r() - Method in class mar.virtualmachine.MarVM
 
shift_r(int, int) - Method in class arche.UP
 
shouldBeCleared() - Method in class physis.core.task.TaskAdapter
Clearing is the default.
shouldBeCleared() - Method in interface physis.core.task.Task
Answers the question: Should the I/O-buffer (@see Metabolism) be cleared after completing this task.
shouldBeCleared() - Method in class physis.core.task.basic.Get
Metabolism cannot be cleared after a simple get task.
shouldBeDeleted() - Method in class physis.core.EnvironmentImpl
Answers the question: Should the current divided codetape be deleted one instruction?
shouldBeDeleted() - Method in interface physis.core.Environment
Answers the question: Should the current divided codetape be deleted one instruction?
shouldBeDeleted() - Method in class physis.core.virtualmachine.PhysisVMTracer
Answers the question: Should the current divided codetape be deleted one instruction?
shouldBeExecuted(long) - Method in class physis.core.triggers.TriggerImpl
If the current update number equals the next time then it should execute.
shouldBeExecuted(long) - Method in interface physis.core.triggers.Trigger
Returns true if the trigger should be executed.
shouldBeInserted() - Method in class physis.core.EnvironmentImpl
Answers the question: Should the current divided codetape be inserted extra instructions?
shouldBeInserted() - Method in interface physis.core.Environment
Answers the question: Should the current divided codetape be inserted extra instructions?
shouldBeInserted() - Method in class physis.core.virtualmachine.PhysisVMTracer
Answers the question: Should the current divided codetape be inserted extra instructions?
shouldBeRemoved() - Method in class physis.core.triggers.TriggerImpl
If it's not periodical or it passed its end value then it should be removed.
shouldBeRemoved() - Method in interface physis.core.triggers.Trigger
Returns true if the trigger should be removed from the active triggers-container.
size - Variable in class physis.core.virtualmachine.InstructionSet
 
size - Variable in class physis.core.virtualmachine.SoupGeneticCodeTape
The size of the codetape.
size - Variable in class arche.Stack
 
size - Variable in class arche.Queue
 
SIZE - Static variable in class physis.core.lifespace.MemoryPoolLifeSpace
 
size() - Method in class physis.core.genotype.Genome
 
snapshot - Variable in class physis.core.genotype.GeneticSnapshot
 
snapshot - Variable in class physis.core.triggers.GeneticSnapshotTrigger
 
socket - Variable in class physis.core.RemoteDigitalOrganism
The socket used for the DOTP commmunication with a remote Digital Org proxy.
Sort - class physis.core.task.advanced.Sort.
 
Sort() - Constructor for class physis.core.task.advanced.Sort
 
SoupGeneticCodeTape - class physis.core.virtualmachine.SoupGeneticCodeTape.
All organisms share one large memory pool.
SoupGeneticCodeTape(int, int) - Constructor for class physis.core.virtualmachine.SoupGeneticCodeTape
 
SoupGeneticCodeTape(String) - Constructor for class physis.core.virtualmachine.SoupGeneticCodeTape
It reads the instructions from a file.The first organism is created this way.(One instruction per line, lines beginning with # are discarded.
SoupLifeSpace - interface physis.core.lifespace.SoupLifeSpace.
Marker interface for soup based lifespaces.
south - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
SOUTH - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
south_server - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
sp - Variable in class arche.Stack
The stack pointer.
SP - Variable in class mar.virtualmachine.MarVM
stack_pointer, it points to the next available element, also equals with stacksize
SP - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SPAWN_THRESHOLD - Static variable in class physis.core.genotype.GeneBank
 
spectrum - Variable in class physis.visualisation.panels.SpectrumIndicatorPanel
 
SpectrumIndicatorPanel - class physis.visualisation.panels.SpectrumIndicatorPanel.
 
SpectrumIndicatorPanel(ColorRange) - Constructor for class physis.visualisation.panels.SpectrumIndicatorPanel
 
spindpanel - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
SPWN - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
Square - class physis.core.task.math.Square.
 
Square() - Constructor for class physis.core.task.math.Square
 
ssize - Variable in class arche.UP
 
stack - Variable in class mar.virtualmachine.MarVM
 
stack - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
stack - Variable in class arche.Stack
 
Stack - class arche.Stack.
Stack as a structural element for processors.
STACK_SIZE - Static variable in class mar.virtualmachine.MarVM
Size of the internal stack.
STACK_SIZE - Static variable in class psoup.virtualmachine.PrimordialSoupVM
Size of the internal stack.
Stack(int) - Constructor for class arche.Stack
 
stackClear() - Method in class mar.virtualmachine.MarVM
 
stackEmpty() - Method in class mar.virtualmachine.MarVM
 
stackFull() - Method in class mar.virtualmachine.MarVM
 
stackPop() - Method in class mar.virtualmachine.MarVM
 
stackPush(int) - Method in class mar.virtualmachine.MarVM
 
stackTop() - Method in class mar.virtualmachine.MarVM
 
start - Variable in class physis.core.triggers.TriggerImpl
 
statistics - Variable in class physis.core.PHYSIS
The statistics-generator subsystem.
Statistics - interface physis.core.statistics.Statistics.
 
STATISTICS_CONFIGURATION - Variable in class physis.core.statistics.StatisticsImpl
 
STATISTICS_DATA_FILE - Variable in class physis.core.statistics.StatisticsImpl
 
StatisticsFactory - class physis.core.statistics.StatisticsFactory.
 
StatisticsFactory() - Constructor for class physis.core.statistics.StatisticsFactory
 
StatisticsImpl - class physis.core.statistics.StatisticsImpl.
Writes statistical information to a file.
StatisticsImpl(Population) - Constructor for class physis.core.statistics.StatisticsImpl
 
status(String) - Static method in class physis.log.Log
 
step - Variable in class physis.core.triggers.TriggerImpl
 
Storage - class arche.Storage.
The abstraction of a processor's hardware structural elements.
STORAGE_ARRAY_SIZE - Static variable in class arche.UP
 
Storage() - Constructor for class arche.Storage
 
StorageArray - class arche.StorageArray.
The hardware memory-array that can be divided for the structural elements.
StorageArray(int) - Constructor for class arche.StorageArray
 
StorageFactory - class arche.StorageFactory.
 
StorageFactory() - Constructor for class arche.StorageFactory
 
STORE - Static variable in class arche.UP
 
store(int, int) - Method in class arche.UP
Writes data to memory from the source structural element.
storePersistently() - Static method in class physis.core.genotype.GeneBank
 
structural_elements - Variable in class arche.StorageArray
 
sub - Static variable in class mar.virtualmachine.MarVM
 
Sub - class physis.core.task.math.Sub.
 
SUB - Static variable in class arche.UP
 
sub() - Method in class mar.virtualmachine.MarVM
 
Sub() - Constructor for class physis.core.task.math.Sub
 
sub(int, int, int) - Method in class arche.UP
 
SUB1 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SUB2 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SUB3 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
SUB4 - Variable in class psoup.virtualmachine.PrimordialSoupVM
 
swap - Static variable in class mar.virtualmachine.MarVM
 
swap() - Method in class mar.virtualmachine.MarVM
 

T

table - Variable in class physis.core.task.PerformedTasksRegister
The TaskLibrary can directly access this table, that's why it has package visibility.
takeASnapshot() - Method in class physis.core.genotype.GeneticSnapshot
Takes a snapshot by iterating through the whole populaion.
tape - Variable in class physis.core.virtualmachine.PhysisVirtualMachine
This codetape contains the organism's genetic code.
Task - interface physis.core.task.Task.
It represents a task, more specifically a function.
TASK_FILE - Static variable in class physis.core.EnvironmentImpl
 
TASK_FILE - Static variable in class physis.core.virtualmachine.PhysisVMTracer
 
task_lookup_table - Variable in class physis.core.task.TaskLibrary
Taskarrays are mapped by their inputsize and outputsize.
TaskAdapter - class physis.core.task.TaskAdapter.
Provides counting and merit-multiplier handling.Subclasses should override the checkActivity, getInputSize and getOutputSize and possibly the getName method and when clearing is not wanted the shouldBeCleared method.
TaskAdapter() - Constructor for class physis.core.task.TaskAdapter
 
TaskFactory - class physis.core.task.TaskFactory.
 
TaskFactory() - Constructor for class physis.core.task.TaskFactory
 
TaskGroup - class physis.core.task.TaskGroup.
 
TaskGroup(String, Vector) - Constructor for class physis.core.task.TaskGroup
 
taskiterator - Variable in class physis.core.task.TaskGroup
 
TaskIterator - class physis.core.task.TaskIterator.
 
TaskIterator(Task[]) - Constructor for class physis.core.task.TaskIterator
 
tasklibrary - Variable in class physis.core.EnvironmentImpl
 
tasklibrary - Variable in class physis.core.virtualmachine.PhysisVMTracer
 
TaskLibrary - class physis.core.task.TaskLibrary.
 
TaskLibrary() - Constructor for class physis.core.task.TaskLibrary
 
tasks - Variable in class physis.core.task.TaskIterator
 
TEMPERING_MASK_B - Static variable in class physis.core.random.MersenneTwister
 
TEMPERING_MASK_C - Static variable in class physis.core.random.MersenneTwister
 
threads - Variable in class physis.core.virtualmachine.ParallelVirtualMachine
 
timestamp - Variable in class physis.core.genotype.GenomeData
The update number when the genome first occurs in the system.
title - Variable in class physis.visualisation.panels.SpectrumIndicatorPanel
 
top2reg - Static variable in class mar.virtualmachine.MarVM
 
top2reg() - Method in class mar.virtualmachine.MarVM
 
toString() - Method in class physis.core.DigitalOrganismImpl
 
toString() - Method in class physis.core.Population
 
toString() - Method in class physis.core.genotype.GenomeData
 
toString() - Method in class physis.core.genotype.Genome
Returns the string representation of the codetape.
toString() - Method in class physis.core.lifespace.PositionInfo2DLattice
 
toString() - Method in class physis.core.task.TaskLibrary
 
toString() - Method in class physis.core.task.TaskAdapter
 
toString() - Method in class physis.core.task.PerformedTasksRegister
 
toString() - Method in class physis.core.triggers.OrganismExtractTrigger
 
toString() - Method in class physis.core.triggers.ChangeTaskBonusesTrigger
 
toString() - Method in class physis.core.triggers.DisasterTrigger
 
toString() - Method in class physis.core.triggers.GeneticSnapshotTrigger
 
toString() - Method in class physis.core.virtualmachine.CellGeneticCodeTape
Returns the string representation of the codetape.
toString() - Method in class arche.StorageArray
 
toString() - Method in class arche.Register
 
Trigger - interface physis.core.triggers.Trigger.
A trigger is a predefined event which is performed at given time in the system and/or if some conditions occur.
TRIGGER_FILE - Static variable in class physis.core.triggers.Triggers
 
TriggerFactory - class physis.core.triggers.TriggerFactory.
 
TriggerFactory() - Constructor for class physis.core.triggers.TriggerFactory
 
TriggerImpl - class physis.core.triggers.TriggerImpl.
Provides the basic implementation for the trigger classes.
TriggerImpl() - Constructor for class physis.core.triggers.TriggerImpl
 
triggers - Variable in class physis.core.PHYSIS
The container of predefined events, operations.
triggers - Variable in class physis.core.triggers.Triggers
The container array.
Triggers - class physis.core.triggers.Triggers.
This class represents the main container of the triggers.
Triggers() - Constructor for class physis.core.triggers.Triggers
The constructor loads the first trigger file.
Triple - class physis.core.task.math.Triple.
 
Triple() - Constructor for class physis.core.task.math.Triple
 
type - Variable in class physis.core.triggers.OrganismExtractTrigger
 
type - Variable in class physis.core.triggers.DisasterTrigger
 
type - Variable in class physis.core.virtualmachine.Instruction
Every instruction has a type.
type_names - Variable in class physis.core.virtualmachine.InstructionSet
This hashtable stores the typenames of the instruction categories.

U

UP - class arche.UP.
This universal processor is designed to increase the evolvability in Tierra-like systems.
UP() - Constructor for class arche.UP
 
update() - Method in class physis.core.DigitalOrganismImpl
 
update() - Method in class physis.core.RemoteDigitalOrganism
 
update() - Method in class physis.core.Population
Updating the whole population by executing a given average number of instructions in each CPU.
update() - Method in interface physis.core.DigitalOrganism
Updates the organism's state by executing one cpu-cycle.
update(int) - Method in class physis.core.DigitalOrganismImpl
 
update(int) - Method in class physis.core.RemoteDigitalOrganism
 
update(int) - Method in interface physis.core.DigitalOrganism
Updates the organism's state by executing given amount of cpu_cycles.
updatecount - Variable in class physis.core.PHYSIS
Counts the number of updates.
updateState() - Method in class physis.core.Population
This method updates the data which represents the population state.
UPPER_MASK - Static variable in class physis.core.random.MersenneTwister
 
usage() - Static method in class physis.core.virtualmachine.PhysisVMTracer
 

V

view_mode - Variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 
Viewer - interface physis.visualisation.Viewer.
All viewer system should have a class that implements this interface.
viewers - Variable in class physis.core.PHYSIS
Several different viewers can be attached to the system.
VirtualMachine - class physis.core.virtualmachine.VirtualMachine.
It is the base class for all virtual machines, which executes the code tapes.
VirtualMachine() - Constructor for class physis.core.virtualmachine.VirtualMachine
It should have one zero-argument constructor! Because a separate factory instantiates them.
VirtualMachineFactory - class physis.core.virtualmachine.VirtualMachineFactory.
As a Factory this will make the digital-organism-instatiating easy.
VirtualMachineFactory() - Constructor for class physis.core.virtualmachine.VirtualMachineFactory
 
VIVIFY - Static variable in class physis.core.DigitalOrganismProxy
 
vivify(DigitalOrganism, GeneticCodeTape, int) - Method in class physis.core.DigitalOrganismImpl
Makes the organism to be alive.
vivify(DigitalOrganism, GeneticCodeTape, int) - Method in class physis.core.RemoteDigitalOrganism
 
vivify(DigitalOrganism, GeneticCodeTape, int) - Method in interface physis.core.DigitalOrganism
Makes the organism to be alive.
vivify(int) - Method in class physis.core.DigitalOrganismProxy
 
vm - Variable in class physis.core.DigitalOrganismImpl
The "heart" of the organism
vm - Variable in class physis.core.virtualmachine.PhysisVMTracer
 
vm_class_name - Static variable in class physis.core.Configuration
 
VM_CLASS_NAME - Static variable in class physis.core.Configuration
 

W

west - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
WEST - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
west_server - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
write(int, short) - Method in interface physis.core.virtualmachine.CodeTape
Sets the content of the tape on the specified position.
write(int, short) - Method in class physis.core.virtualmachine.SoupGeneticCodeTape
 
write(int, short) - Method in class physis.core.virtualmachine.CellGeneticCodeTape
The position is mapped into the proper range.
write(short) - Method in class arche.Storage
 
write(short) - Method in class arche.Stack
Sets the content to a new value.
write(short) - Method in class arche.Register
Sets the content to a new value.
write(short) - Method in class arche.Queue
Sets the content to a new value.
writeFossils() - Static method in class physis.core.genotype.GeneBank
 

X

x - Variable in class physis.core.iterator.Array2DDigitalOrganismIterator
 
x - Variable in class physis.core.iterator.ArrayDigitalOrganismIterator
 
x - Variable in class physis.core.lifespace.PositionInfo2DLattice
 
x - Variable in class physis.core.task.TaskIterator
 
x_size - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
x_size - Variable in class physis.core.lifespace.Lattice2DLifeSpace
 
X_SIZE - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
X_SIZE - Static variable in class physis.core.lifespace.Lattice2DLifeSpace
 
X_SIZE - Static variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
Properties as in the Lattice2DLifeSpace
xa - Variable in class physis.core.statistics.StatisticsImpl
 
xa_s - Variable in class physis.core.statistics.StatisticsImpl
 
xaer - Variable in class physis.core.statistics.StatisticsImpl
 
xaer_s - Variable in class physis.core.statistics.StatisticsImpl
 
xel - Variable in class physis.core.statistics.StatisticsImpl
 
xel_s - Variable in class physis.core.statistics.StatisticsImpl
 
xeler - Variable in class physis.core.statistics.StatisticsImpl
 
xeler_s - Variable in class physis.core.statistics.StatisticsImpl
 
xf - Variable in class physis.core.statistics.StatisticsImpl
 
xf_s - Variable in class physis.core.statistics.StatisticsImpl
 
xfer - Variable in class physis.core.statistics.StatisticsImpl
 
xfer_s - Variable in class physis.core.statistics.StatisticsImpl
 
xgl - Variable in class physis.core.statistics.StatisticsImpl
 
xgl_s - Variable in class physis.core.statistics.StatisticsImpl
 
xgler - Variable in class physis.core.statistics.StatisticsImpl
 
xgler_s - Variable in class physis.core.statistics.StatisticsImpl
 
xm - Variable in class physis.core.statistics.StatisticsImpl
 
xm_s - Variable in class physis.core.statistics.StatisticsImpl
 
xmer - Variable in class physis.core.statistics.StatisticsImpl
 
xmer_s - Variable in class physis.core.statistics.StatisticsImpl
 
XOR - Static variable in class arche.UP
 
xor(int, int, int) - Method in class arche.UP
 

Y

y - Variable in class physis.core.iterator.Array2DDigitalOrganismIterator
 
y - Variable in class physis.core.lifespace.PositionInfo2DLattice
 
y_size - Variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
y_size - Variable in class physis.core.lifespace.Lattice2DLifeSpace
 
Y_SIZE - Static variable in class physis.core.lifespace.DistributedLattice2DLifeSpace
 
Y_SIZE - Static variable in class physis.core.lifespace.Lattice2DLifeSpace
 
Y_SIZE - Static variable in class physis.visualisation.panels.lifespace.Lattice2DViewer
 

Z

zero - Static variable in class mar.virtualmachine.MarVM
 
zero() - Method in class mar.virtualmachine.MarVM
 

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