physis.core.virtualmachine
Class SoupGeneticCodeTape

java.lang.Object
  |
  +--physis.core.virtualmachine.SoupGeneticCodeTape

All Implemented Interfaces:

CodeTape, GeneticCodeTape

public class SoupGeneticCodeTape

extends java.lang.Object

implements GeneticCodeTape

All organisms share one large memory pool. This allows many interactions between them. (Tierra-like)

Field Summary

protected int	allocated_size
protected boolean	alreadyallocated
protected static byte[]	attributes The attributes array for the memory pool.
protected int	child_loc The child's position.
protected int	child_size The child's size
private static InstructionSet	instruction_set
protected int	loc The location of this codetape in the big pool.
protected static short[]	pool This is the big memory pool.
protected int	size The size of the codetape.

Fields inherited from interface physis.core.virtualmachine.GeneticCodeTape

COPIED, EXECUTED, EXECUTED_OR_COPIED, MUTATED

Constructor Summary

(package private)	SoupGeneticCodeTape(int loc_, int size_)
	SoupGeneticCodeTape(java.lang.String filename) It reads the instructions from a file.The first organism is created this way.(One instruction per line, lines beginning with # are discarded.

Method Summary

void	allocate(int numberof_newcells) It's a biological operator.
boolean	blockCopy(int source, int destination, int length) Copies an instruction from source position to destination position.
int	calculateEffectiveLength() The effective length can be calculated by the number of executed instructions.
void	clearExecutedFlag(int position)
boolean	contains(short instcode) Returns true if the codetape contains the specified instruction.
boolean	copy(int source, int destination) Copies an instruction from source position to destination position.
void	delete() Removes an instruction from a random position.
GeneticCodeTape	divide() It divides the codetape.
short	fetchInst(int position) Simply returns the instruction or operand on the specified position.
Genome	getChildGenome() Returns the genetic information from the codetape.
protected short	getChildInstruction(int position)
Genome	getGenome() Returns the genetic information from the codetape.
int	getSize() Returns the absolute size of the codetape.(number of contained instructions)
void	insert() Inserts an instruction on a random position.
boolean	isAllocated() Returns true if the cell already allocated space for the spawn.
boolean	isAllocationPossible(int numberof_newcells) The size must be in a predefined range, otherwise the allocation fails.
boolean	isCopied(int position) Answers the question: is the positionth instruction copied?
boolean	isExecuted(int position) Answers the question: is the positionth instruction executed?
boolean	isMutated(int position) Answers the question: is the positionth instruction mutated?
boolean	isProliferationPossible() Checks whether the organism is able to spawn (are there enough copied instructions?).
void	mutate(int position) Mutate the specified instruction.
short	read(int position) It gives the instruction on the specified position.
int	searchBackward(int start, short code, int depth)
int	searchForward(int start, short code, int depth)
void	write(int position, short new_value) Sets the content of the tape on the specified position.

Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait

Field Detail

instruction_set

private static InstructionSet instruction_set

pool

protected static short[] pool

This is the big memory pool. Only one could exist.

attributes

protected static byte[] attributes

The attributes array for the memory pool.

loc

protected int loc

The location of this codetape in the big pool. Pointer to the first instruction.

size

protected int size

The size of the codetape. The position of the last instruction: loc + size - 1.

allocated_size

protected int allocated_size

alreadyallocated

protected boolean alreadyallocated

child_loc

protected int child_loc

The child's position.

child_size

protected int child_size

The child's size

Constructor Detail

SoupGeneticCodeTape

public SoupGeneticCodeTape(java.lang.String filename)

It reads the instructions from a file.The first organism is created this way.(One instruction per line, lines beginning with # are discarded.

SoupGeneticCodeTape

SoupGeneticCodeTape(int loc_,
                    int size_)

Method Detail

read

public short read(int position)

It gives the instruction on the specified position. SIDE EFFECT!!! The executed flag is set!

Specified by:

read in interface CodeTape

fetchInst

public short fetchInst(int position)

Description copied from interface: GeneticCodeTape

Simply returns the instruction or operand on the specified position.
The position becomes EXECUTED.
This method isn't failsafe like read and write. The virtualmachine has to take care of the proper position. It provides only quick access for the executable part of the code.

Specified by:

fetchInst in interface GeneticCodeTape

write

public void write(int position,
                  short new_value)

Description copied from interface: CodeTape

Sets the content of the tape on the specified position. ALWAYS DOES SOMETHING! There shouldn't be any unhandled error situation!

Specified by:

write in interface CodeTape

clearExecutedFlag

public void clearExecutedFlag(int position)

Specified by:

clearExecutedFlag in interface GeneticCodeTape

isAllocationPossible

public boolean isAllocationPossible(int numberof_newcells)

Description copied from interface: GeneticCodeTape

The size must be in a predefined range, otherwise the allocation fails.

Specified by:

isAllocationPossible in interface GeneticCodeTape

allocate

public void allocate(int numberof_newcells)

Description copied from interface: GeneticCodeTape

It's a biological operator. This should happen before the cell division. (making room, preparating or something like that) CELL: It allocates instruction cells at the end of the codetape. One allocation may occur between divides. It also allocates the information arrays (iscopied...etc.) SOUP: Because of the one large memory pool (soup) there's no space allocation. In this case it's only the declaration of the size of the code block to be copied.

Specified by:

allocate in interface GeneticCodeTape

isAllocated

public boolean isAllocated()

Description copied from interface: GeneticCodeTape

Returns true if the cell already allocated space for the spawn.

Specified by:

isAllocated in interface GeneticCodeTape

isProliferationPossible

public boolean isProliferationPossible()

Description copied from interface: GeneticCodeTape

Checks whether the organism is able to spawn (are there enough copied instructions?).

Specified by:

isProliferationPossible in interface GeneticCodeTape

divide

public GeneticCodeTape divide()

Description copied from interface: GeneticCodeTape

It divides the codetape. The Environment is responsible for palcing the child, the codetape only returns an other one.

Specified by:

divide in interface GeneticCodeTape

mutate

public void mutate(int position)

Description copied from interface: GeneticCodeTape

Mutate the specified instruction.

Specified by:

mutate in interface GeneticCodeTape

isMutated

public boolean isMutated(int position)

Description copied from interface: GeneticCodeTape

Answers the question: is the positionth instruction mutated?

Specified by:

isMutated in interface GeneticCodeTape

isCopied

public boolean isCopied(int position)

Description copied from interface: GeneticCodeTape

Answers the question: is the positionth instruction copied?

Specified by:

isCopied in interface GeneticCodeTape

isExecuted

public boolean isExecuted(int position)

Description copied from interface: GeneticCodeTape

Answers the question: is the positionth instruction executed?

Specified by:

isExecuted in interface GeneticCodeTape

copy

public boolean copy(int source,
                    int destination)

Description copied from interface: GeneticCodeTape

Copies an instruction from source position to destination position. Returns true if the copy was succesfull.

Specified by:

copy in interface GeneticCodeTape

blockCopy

public boolean blockCopy(int source,
                         int destination,
                         int length)

Description copied from interface: GeneticCodeTape

Copies an instruction from source position to destination position. Returns true if the copy was succesfull.

Specified by:

blockCopy in interface GeneticCodeTape

insert

public void insert()

Inserts an instruction on a random position.

Specified by:

insert in interface GeneticCodeTape

delete

public void delete()

Removes an instruction from a random position.

Specified by:

delete in interface GeneticCodeTape

getSize

public int getSize()

Description copied from interface: GeneticCodeTape

Returns the absolute size of the codetape.(number of contained instructions)

Specified by:

getSize in interface GeneticCodeTape

contains

public boolean contains(short instcode)

Description copied from interface: GeneticCodeTape

Returns true if the codetape contains the specified instruction.

Specified by:

contains in interface GeneticCodeTape

Following copied from interface: physis.core.virtualmachine.GeneticCodeTape

Parameters:

instcode - The searched instruction.

searchForward

public int searchForward(int start,
                         short code,
                         int depth)

searchBackward

public int searchBackward(int start,
                          short code,
                          int depth)

calculateEffectiveLength

public int calculateEffectiveLength()

The effective length can be calculated by the number of executed instructions.

Specified by:

calculateEffectiveLength in interface GeneticCodeTape

getGenome

public Genome getGenome()

Returns the genetic information from the codetape.

Specified by:

getGenome in interface GeneticCodeTape

getChildGenome

public Genome getChildGenome()

Returns the genetic information from the codetape.

Specified by:

getChildGenome in interface GeneticCodeTape

getChildInstruction

protected short getChildInstruction(int position)