Module io.jenetics.prog

Package io.jenetics.prog

Class ProgramChromosome<A>

java.lang.Object

io.jenetics.AbstractChromosome<ProgramGene<A>>

io.jenetics.ext.AbstractTreeChromosome<Op<A>,ProgramGene<A>>

io.jenetics.prog.ProgramChromosome<A>

All Implemented Interfaces:

Chromosome<ProgramGene<A>>, TreeChromosome<Op<A>,ProgramGene<A>>, BaseSeq<ProgramGene<A>>, Factory<Chromosome<ProgramGene<A>>>, Verifiable, Serializable, Iterable<ProgramGene<A>>, Function<A[],A>, RandomAccess

public class ProgramChromosome<A>
extends AbstractTreeChromosome<Op<A>,ProgramGene<A>>
implements Function<A[],A>, Serializable

Holds the nodes of the operation tree.

final int depth = 6;
final ISeq<Op<Double>> operations = ISeq.of(...);
final ISeq<Op<Double>> terminals = ISeq.of(...);
final ProgramChromosome<Double> ch = ProgramChromosome.of(
    depth,
    // If the program has more than 200 nodes, it is marked as "invalid".
    ch -> ch.length() <= 200,
    operations,
    terminals
);

Since:

3.9

Version:

4.1

See Also:

• Serialized Form

Field Summary

Fields inherited from class io.jenetics.AbstractChromosome

_genes, _valid

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	ProgramChromosome(ISeq<ProgramGene<A>> program, Predicate<? super ProgramChromosome<A>> validator, ISeq<? extends Op<A>> operations, ISeq<? extends Op<A>> terminals)	Create a new program chromosome from the given program genes.

Method Summary

Modifier and Type	Method	Description
A	apply(A[] args)	Evaluates the root node of this chromosome.
final A	eval(A... args)	Evaluates the root node of this chromosome.
boolean	isValid()	Check if this object is valid.
ProgramChromosome<A>	newInstance()	Create a new instance of type T.
ProgramChromosome<A>	newInstance(ISeq<ProgramGene<A>> genes)	A factory method which creates a new Chromosome of specific type and the given genes.
static <A> ProgramChromosome<A>	of(int depth, ISeq<? extends Op<A>> operations, ISeq<? extends Op<A>> terminals)	Create a new program chromosome with the defined depth.
static <A> ProgramChromosome<A>	of(int depth, Predicate<? super ProgramChromosome<A>> validator, ISeq<? extends Op<A>> operations, ISeq<? extends Op<A>> terminals)	Create a new program chromosome with the defined depth.
static <A> ProgramChromosome<A>	of(Tree<? extends Op<A>,?> program, ISeq<? extends Op<A>> operations, ISeq<? extends Op<A>> terminals)	Create a new chromosome from the given operation tree (program).
static <A> ProgramChromosome<A>	of(Tree<? extends Op<A>,?> program, Predicate<? super ProgramChromosome<A>> validator, ISeq<? extends Op<A>> operations, ISeq<? extends Op<A>> terminals)	Create a new chromosome from the given operation tree (program).
static <A> ProgramChromosome<A>	of(ISeq<ProgramGene<A>> genes, ISeq<? extends Op<A>> operations, ISeq<? extends Op<A>> terminals)
static <A> ProgramChromosome<A>	of(ISeq<ProgramGene<A>> genes, Predicate<? super ProgramChromosome<A>> validator, ISeq<? extends Op<A>> operations, ISeq<? extends Op<A>> terminals)	Create a new program chromosome from the given (flattened) program tree.
ISeq<Op<A>>	operations()	Return the allowed operations.
ISeq<Op<A>>	terminals()	Return the allowed terminal operations.

Methods inherited from class io.jenetics.AbstractChromosome

equals, get, hashCode, length, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface io.jenetics.util.BaseSeq

forEach, get, isEmpty, iterator, length, listIterator, nonEmpty, spliterator, stream

Methods inherited from interface io.jenetics.Chromosome

as, gene

Methods inherited from interface io.jenetics.util.Factory

instances

Methods inherited from interface java.util.function.Function

andThen, compose

Methods inherited from interface io.jenetics.ext.TreeChromosome

root

Constructor Details

ProgramChromosome

protected ProgramChromosome(ISeq<ProgramGene<A>> program,
 Predicate<? super ProgramChromosome<A>> validator,
 ISeq<? extends Op<A>> operations,
 ISeq<? extends Op<A>> terminals)

Create a new program chromosome from the given program genes. This constructor assumes that the given program is valid. Since the program validation is quite expensive, the validity check is skipped in this constructor.

Parameters:

program - the program. During the program evolution, newly created program trees have the same depth than this tree.

validator - the chromosome validator. A typical validator would check the size of the tree and if the tree is too large, mark it at invalid. The validator may be null.

operations - the allowed non-terminal operations

terminals - the allowed terminal operations

Throws:

NullPointerException - if one of the given arguments is null

IllegalArgumentException - if either the operations or terminals sequence is empty

Method Details

operations

public ISeq<Op<A>> operations()

Return the allowed operations.

Returns:

the allowed operations

Since:

5.0

terminals

public ISeq<Op<A>> terminals()

Return the allowed terminal operations.

Returns:

the allowed terminal operations

Since:

5.0

isValid

public boolean isValid()

Description copied from interface: Verifiable

Check if this object is valid.

Specified by:

isValid in interface Chromosome<A>

Specified by:

isValid in interface Verifiable

Overrides:

isValid in class AbstractChromosome<ProgramGene<A>>

Returns:

true if this object is valid, false otherwise.

apply

public A apply(A[] args)

Evaluates the root node of this chromosome.

Specified by:

apply in interface Function<A[],A>

Parameters:

args - the input variables

Returns:

the evaluated value

Throws:

NullPointerException - if the given variable array is null

See Also:

• ProgramGene.apply(Object[])
• eval(Object[])

eval

@SafeVarargs
public final A eval(A... args)

Evaluates the root node of this chromosome.

Parameters:

args - the function arguments

Returns:

the evaluated value

Throws:

NullPointerException - if the given variable array is null

See Also:

• ProgramGene.eval(Object[])
• apply(Object[])

newInstance

public ProgramChromosome<A> newInstance(ISeq<ProgramGene<A>> genes)

Description copied from interface: Chromosome

A factory method which creates a new Chromosome of specific type and the given genes.

Specified by:

newInstance in interface Chromosome<A>

Parameters:

genes - the genes of the new chromosome. The given genes array is not copied.

Returns:

A new Chromosome of the same type with the given genes.

newInstance

public ProgramChromosome<A> newInstance()

Description copied from interface: Factory

Create a new instance of type T.

Specified by:

newInstance in interface Factory<A>

Returns:

a new instance of type T

of

public static <A> ProgramChromosome<A> of(Tree<? extends Op<A>,?> program,
 Predicate<? super ProgramChromosome<A>> validator,
 ISeq<? extends Op<A>> operations,
 ISeq<? extends Op<A>> terminals)

Create a new chromosome from the given operation tree (program).

Type Parameters:

A - the operation type

Parameters:

program - the operation tree

validator - the chromosome validator. A typical validator would check the size of the tree and if the tree is too large, mark it at invalid. The validator may be null.

operations - the allowed non-terminal operations

terminals - the allowed terminal operations

Returns:

a new chromosome from the given operation tree

Throws:

NullPointerException - if one of the given arguments is null

IllegalArgumentException - if the given operation tree is invalid, which means there is at least one node where the operation arity and the node child count differ.

of

public static <A> ProgramChromosome<A> of(Tree<? extends Op<A>,?> program,
 ISeq<? extends Op<A>> operations,
 ISeq<? extends Op<A>> terminals)

Create a new chromosome from the given operation tree (program).

Type Parameters:

A - the operation type

Parameters:

program - the operation tree

operations - the allowed non-terminal operations

terminals - the allowed terminal operations

Returns:

a new chromosome from the given operation tree

Throws:

NullPointerException - if one of the given arguments is null

IllegalArgumentException - if the given operation tree is invalid, which means there is at least one node where the operation arity and the node child count differ.

of

public static <A> ProgramChromosome<A> of(int depth,
 Predicate<? super ProgramChromosome<A>> validator,
 ISeq<? extends Op<A>> operations,
 ISeq<? extends Op<A>> terminals)

Create a new program chromosome with the defined depth. This method will create a full program tree.

Type Parameters:

A - the operation type

Parameters:

depth - the depth of the created program tree

validator - the chromosome validator. A typical validator would check the size of the tree and if the tree is too large, mark it at invalid. The validator may be null.

operations - the allowed non-terminal operations

terminals - the allowed terminal operations

Returns:

a new program chromosome from the given (flattened) program tree

Throws:

NullPointerException - if one of the parameters is null

IllegalArgumentException - if the depth is smaller than zero

of

public static <A> ProgramChromosome<A> of(int depth,
 ISeq<? extends Op<A>> operations,
 ISeq<? extends Op<A>> terminals)

Create a new program chromosome with the defined depth. This method will create a full program tree.

Type Parameters:

A - the operation type

Parameters:

depth - the depth of the created (full) program tree

operations - the allowed non-terminal operations

terminals - the allowed terminal operations

Returns:

a new program chromosome from the given (flattened) program tree

Throws:

NullPointerException - if one of the parameters is null

IllegalArgumentException - if the depth is smaller than zero

of

public static <A> ProgramChromosome<A> of(ISeq<ProgramGene<A>> genes,
 Predicate<? super ProgramChromosome<A>> validator,
 ISeq<? extends Op<A>> operations,
 ISeq<? extends Op<A>> terminals)

Create a new program chromosome from the given (flattened) program tree. This method doesn't make any assumption about the validity of the given operation tree. If the tree is not valid, it will repair it. This behaviour allows the safe usage of all existing alterers.

final ProgramChromosome<Double> ch = ProgramChromosome.of(
    genes,
    // If the program has more that 200 nodes, it is marked as "invalid".
    ch -> ch.length() <= 200,
    operations,
    terminals
);

Type Parameters:

A - the operation type

Parameters:

genes - the program genes

validator - the chromosome validator to use

operations - the allowed non-terminal operations

terminals - the allowed terminal operations

Returns:

a new program chromosome from the given (flattened) program tree

Throws:

NullPointerException - if one of the parameters is null

of

public static <A> ProgramChromosome<A> of(ISeq<ProgramGene<A>> genes,
 ISeq<? extends Op<A>> operations,
 ISeq<? extends Op<A>> terminals)