Chromosome

java.lang.Object
- jcgp.backend.population.Chromosome

All Implemented Interfaces:

java.lang.Comparable<Chromosome>
```
public class Chromosome
extends java.lang.Object
implements java.lang.Comparable<Chromosome>
```
This class encapsulates a CGP chromosome.

A chromosome contains a matrix of nodes and arrays of inputs and outputs. These elements are all interconnected, and actually form the chromosome network itself. Individual nodes can be retrieved using getNode() which requires the row and column to be specified. The same works for inputs and outputs using the associated getters, in which case only the index is necessary.

In evolutionary computation it is often necessary to make copies of chromosomes; this can be accomplished in JCGP in two ways. The recommended way to do this is using copyChromosome() in Population, but alternatively it can be done by using the Chromosome copy constructor and specifying the object to copy from, or by using the copyGenes() method.

To illustrate this, given two chromosomes, chr1 and chr2, the following code:

chr1.copyGenes(chr2);

will modify all of chr1's connections and functions to match those of chr2, without creating a new instance. In contrast,

chr1 = new Chromosome(chr2);

creates a new instance of chromosome which is identical to chr2 and assigns it to chr1, meaning any old references to chr1 that are not updated will still refer to a chromosome that is not identical to chr2. In practice, the most reliable way is to use the copy method in Population. Assuming chr1 and chr2 are indexed 1 and 2 in population respectively,

population.copyChromosome(2, 1);

will copy chr2 into chr1 without creating new instances or requiring access to the underlying chromosome array. Chromosome offers a variety of methods to compare chromosomes as well, such as compareGenesTo() and compareActiveGenesTo(). Comparable is implemented to compare fitness value, meaning compareTo() returns a value depending the relative fitness of the compared chromosomes.

In order to set the chromosome's input values for decoding, setInputs() should be used. A few utility methods are provided in order to retrieve random elements from the chromosome, which are used internally to initialise with random connections but also externally by mutators when performing mutations.

Author:

Eduardo Pedroni

Constructor Summary

Constructors
Constructor and Description

Chromosome(Chromosome clone)
Copy constructor.

Chromosome(Resources resources)
Initialise a chromosome with the specified parameters.

Constructors
Constructor and Description
`Chromosome(Chromosome clone)` Copy constructor.
`Chromosome(Resources resources)` Initialise a chromosome with the specified parameters.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`compareActiveGenesTo(Chromosome chromosome)` Does the same as `compareGenesto()` but only looks at the active portion of the chromosome.
`boolean`	`compareGenesTo(Chromosome chromosome)` Performs a deep comparison between this chromosome and the provided one.
`int`	`compareTo(Chromosome o)`
`void`	`copyGenes(Chromosome clone)` Creates a deep copy of the specified chromosome in the this instance.
`java.util.ArrayList<Node>`	`getActiveNodes()` This method computes a list of active nodes (if necessary) and returns it.
`double`	`getFitness()`
`Input`	`getInput(int index)` Returns a reference to the indexed input.
`Node`	`getNode(int row, int column)` Returns a reference to any node, addressed by row and column.
`Output`	`getOutput(int index)` Returns a reference to the indexed output.
`Connection`	`getRandomConnection()` This method will pick a completely random connection, independently of levels back, including inputs.
`Connection`	`getRandomConnection(int column)` Returns a random allowed connection respecting levels back. This method may always pick inputs, as they can be picked regardless of the column.
`Mutable`	`getRandomMutable()` This method is useful for mutating chromosomes.
`Resources`	`getResources()`
`void`	`printNodes()` Iterates through the nodes and prints all connections and functions.
`void`	`recomputeActiveNodes()` This causes the list of active nodes to be recomputed lazily (once it is actually requested).
`void`	`reinitialiseConnections()` Sets random connections and functions across the entire chromosome.
`void`	`setFitness(double newFitness)` Sets the fitness of the chromosome.
`void`	`setInputs(java.lang.Object... values)` Loops through the inputs and sets the specified values, so that evaluations can be performed.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - Chromosome
```
public Chromosome(Resources resources)
```
    Initialise a chromosome with the specified parameters. Random valid connections are created upon initialisation.
    
    Parameters:
    
    resources - the experiment's resources.
  - Chromosome
```
public Chromosome(Chromosome clone)
```
    Copy constructor. Initialise a new chromosome with the exact same connections as a given instance of Chromosome.
    
    Parameters:
    
    clone - the chromosome to be copied.
- Method Detail
  - reinitialiseConnections
```
public void reinitialiseConnections()
```
    Sets random connections and functions across the entire chromosome. This method can be used more than once for each instance, if entirely random chromosomes are desired.
  - copyGenes
```
public void copyGenes(Chromosome clone)
```
    Creates a deep copy of the specified chromosome in the this instance. In practice, this iterates through the entire chromosome making equivalent connections and setting functions to the same values as those in the specified chromosome. It also sets the fitness of the copy to the same value as the original.
    It is assumed that both chromosomes have the same topology; while this method will still run if that is not the case, the effects might be undesirable and null pointer access might occur.
    
    Parameters:
    
    clone - the chromosome to clone.
  - getNode
```
public Node getNode(int row,
                    int column)
```
    Returns a reference to any node, addressed by row and column.
    
    Parameters:
    
    row - the row of the node.
    
    column - the column of the node.
    
    Returns:
    
    the addressed node.
  - getOutput
```
public Output getOutput(int index)
```
    Returns a reference to the indexed output.
    
    Parameters:
    
    index - the output index.
    
    Returns:
    
    the output reference.
  - getInput
```
public Input getInput(int index)
```
    Returns a reference to the indexed input.
    
    Parameters:
    
    index - the input index.
    
    Returns:
    
    the input reference.
  - getFitness
```
public double getFitness()
```
    Returns:
    
    the fitness of the chromosome.
  - setFitness
```
public void setFitness(double newFitness)
```
    Sets the fitness of the chromosome. This method should be used by the experiment problem when the population is evaluated in order to assign a fitness to each individual.
    
    Parameters:
    
    newFitness - the fitness to assign.
  - setInputs
```
public void setInputs(java.lang.Object... values)
```
    Loops through the inputs and sets the specified values, so that evaluations can be performed. If the number of elements in the array of values does not match the number of inputs exactly, an exception is thrown.
    
    Parameters:
    
    values - the values the input should take.
  - getRandomMutable
```
public Mutable getRandomMutable()
```
    This method is useful for mutating chromosomes. It returns any random Mutable out of the chromosome with equal probability.
    
    Returns:
    
    a random element that can be mutated - node or output.
  - getRandomConnection
```
public Connection getRandomConnection(int column)
```
    Returns a random allowed connection respecting levels back.
    This method may always pick inputs, as they can be picked regardless of the column.
    
    Parameters:
    
    column - the column to use as reference.
    
    Returns:
    
    a random connection.
  - getRandomConnection
```
public Connection getRandomConnection()
```
    This method will pick a completely random connection, independently of levels back, including inputs. It is useful for setting outputs.
    
    Returns:
    
    a random connection regardless of levels back.
  - recomputeActiveNodes
```
public void recomputeActiveNodes()
```
    This causes the list of active nodes to be recomputed lazily (once it is actually requested).
  - getActiveNodes
```
public java.util.ArrayList<Node> getActiveNodes()
```
    This method computes a list of active nodes (if necessary) and returns it.
    
    Returns:
    
    the list of active nodes.
  - compareGenesTo
```
public boolean compareGenesTo(Chromosome chromosome)
```
    Performs a deep comparison between this chromosome and the provided one. This is done on a gene-by-gene basis. This method returns true if and only if:
    - the chromosomes being compared are not the same instance;
    - the connections of the compared chromosomes are not the same instance;
    - the grid position of the chromosome's elements are the same;
    The relationship computed by this method is:
    - symmetric: a.copyOf(b) == b.copyOf(a);
    - not reflexive: a.copyOf(a) returns false;
    - not transitive: if a.copyOf(b) is true and b.copyOf(c) is true, a.copyOf(c) is not necessarily true since it is possible that a == c.
    Parameters:
    
    chromosome - the chromosome to compare to.
    
    Returns:
    
    true if it is a copy of this chromosome, but not the same chromosome.
  - compareActiveGenesTo
```
public boolean compareActiveGenesTo(Chromosome chromosome)
```
    Does the same as compareGenesto() but only looks at the active portion of the chromosome.
    
    Parameters:
    
    chromosome - the chromosome to compare to.
    
    Returns:
    
    true if the two active portions are identical.
  - printNodes
```
public void printNodes()
```
    Iterates through the nodes and prints all connections and functions. This is intended for debugging purposes only and does not print to the GUI console.
  - getResources
```
public Resources getResources()
```
    Returns:
    
    a reference to the resources based on which the chromosome was built.
  - compareTo
```
public int compareTo(Chromosome o)
```
    Specified by:
    
    compareTo in interface java.lang.Comparable<Chromosome>

Class Chromosome

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Chromosome

Chromosome

Method Detail

reinitialiseConnections

copyGenes

getNode

getOutput

getInput

getFitness

setFitness

setInputs

getRandomMutable

getRandomConnection

getRandomConnection

recomputeActiveNodes

getActiveNodes

compareGenesTo

compareActiveGenesTo

printNodes

getResources

compareTo