Date: Tue, 6 May 2014 14:29:37 +0100 Subject: Added javadocs, made minor changes to the comments --- doc/jcgp/backend/population/Chromosome.html | 742 +++++++++++++++++++++ doc/jcgp/backend/population/Connection.html | 249 +++++++ doc/jcgp/backend/population/Gene.html | 241 +++++++ doc/jcgp/backend/population/Input.html | 361 ++++++++++ doc/jcgp/backend/population/MutableElement.html | 306 +++++++++ doc/jcgp/backend/population/Node.html | 544 +++++++++++++++ doc/jcgp/backend/population/Output.html | 447 +++++++++++++ doc/jcgp/backend/population/Population.html | 411 ++++++++++++ .../backend/population/class-use/Chromosome.html | 340 ++++++++++ .../backend/population/class-use/Connection.html | 301 +++++++++ doc/jcgp/backend/population/class-use/Gene.html | 194 ++++++ doc/jcgp/backend/population/class-use/Input.html | 187 ++++++ .../population/class-use/MutableElement.html | 228 +++++++ doc/jcgp/backend/population/class-use/Node.html | 244 +++++++ doc/jcgp/backend/population/class-use/Output.html | 202 ++++++ .../backend/population/class-use/Population.html | 265 ++++++++ doc/jcgp/backend/population/package-frame.html | 29 + doc/jcgp/backend/population/package-summary.html | 196 ++++++ doc/jcgp/backend/population/package-tree.html | 146 ++++ doc/jcgp/backend/population/package-use.html | 338 ++++++++++ 20 files changed, 5971 insertions(+) create mode 100644 doc/jcgp/backend/population/Chromosome.html create mode 100644 doc/jcgp/backend/population/Connection.html create mode 100644 doc/jcgp/backend/population/Gene.html create mode 100644 doc/jcgp/backend/population/Input.html create mode 100644 doc/jcgp/backend/population/MutableElement.html create mode 100644 doc/jcgp/backend/population/Node.html create mode 100644 doc/jcgp/backend/population/Output.html create mode 100644 doc/jcgp/backend/population/Population.html create mode 100644 doc/jcgp/backend/population/class-use/Chromosome.html create mode 100644 doc/jcgp/backend/population/class-use/Connection.html create mode 100644 doc/jcgp/backend/population/class-use/Gene.html create mode 100644 doc/jcgp/backend/population/class-use/Input.html create mode 100644 doc/jcgp/backend/population/class-use/MutableElement.html create mode 100644 doc/jcgp/backend/population/class-use/Node.html create mode 100644 doc/jcgp/backend/population/class-use/Output.html create mode 100644 doc/jcgp/backend/population/class-use/Population.html create mode 100644 doc/jcgp/backend/population/package-frame.html create mode 100644 doc/jcgp/backend/population/package-summary.html create mode 100644 doc/jcgp/backend/population/package-tree.html create mode 100644 doc/jcgp/backend/population/package-use.html (limited to 'doc/jcgp/backend/population') diff --git a/doc/jcgp/backend/population/Chromosome.html b/doc/jcgp/backend/population/Chromosome.html new file mode 100644 index 0000000..ffcb6f8 --- /dev/null +++ b/doc/jcgp/backend/population/Chromosome.html @@ -0,0 +1,742 @@ + + + + + +Chromosome + + + + + + + + +

+ + +

+ + + +

Prev Class
Next Class

Frames
No Frames

All Classes

+ +

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

+ + +

+ + + +

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.
+
+

+ +

+ + +

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. +
`MutableElement`	`getRandomMutableElement()` + 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.
    +
    +
  + + + +
  - +
    getRandomMutableElement
    +
```
public MutableElement getRandomMutableElement()
```
    +
    This method is useful for mutating chromosomes. It returns any + random MutableElement 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>
    +
    +
  +
+

+ + +

Modifier and Type	Method and Description
`int`	`getIndex()`
`java.lang.Object`	`getValue()` + Compute and return the value of this connection. +
`void`	`setValue(java.lang.Object newValue)` + Sets this input's value. +
`java.lang.String`	`toString()`

Modifier and Type	Method and Description
`boolean`	`copyOf(MutableElement element)` + Asserts if the specified element is a copy of the elements + this is called on. + This method returns true if and only if: + + the elements being compared are not the same instance; + the connections of the compared elements are not the same instance; + the elements have the same function (in the case of Node); + the grid position of the elements themselves are the same; + the grid position of all equivalent connections 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. + +
`void`	`setConnection(int index, + Connection newConnection)` + This method sets the indexed connection to the specified new connection. +

Modifier and Type	Method and Description
`java.lang.Object`	`calculate()`
`boolean`	`copyOf(MutableElement m)` + Asserts if the specified element is a copy of the elements + this is called on. + This method returns true if and only if: + + the elements being compared are not the same instance; + the connections of the compared elements are not the same instance; + the elements have the same function (in the case of Node); + the grid position of the elements themselves are the same; + the grid position of all equivalent connections 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. + +
`void`	`getActiveNodes(java.util.ArrayList<Node> activeNodes)`
`int`	`getIndex()`
`Connection`	`getSource()`
`void`	`setConnection(int index, + Connection newConnection)` + When mutating an output, the index parameter + is simply ignored and the output source is + set. +
`java.lang.String`	`toString()`

Modifier and Type	Method and Description
`void`	`copyChromosome(int source, + int target)` + Copy a chromosome into a different position. +
`Chromosome`	`get(int index)` + Returns the indexed chromosome. +
`Chromosome`	`getRandomChromosome()`
`void`	`reinitialise()` + Loop through all chromosomes and randomise all connections + and functions. +
`void`	`sort()` + Sorts the population in ascending order of fitness quality. +

Package	Description
jcgp.backend.modules.mutator
jcgp.backend.parsers
jcgp.backend.population
jcgp.gui.population

Modifier and Type	Method and Description
`void`	ProbabilisticMutator.`mutate(Chromosome chromosome)`
`abstract void`	Mutator.`mutate(Chromosome chromosome)` + Applies mutations to the specified chromosome according + to the parameter values. +
`void`	PointMutator.`mutate(Chromosome chromosome)`

Modifier and Type	Method and Description
`static void`	ChromosomeParser.`parse(java.io.File file, + Chromosome chromosome, + Resources resources)` + Use this method to parse .chr files into a given chromosome. +
`static void`	ChromosomeParser.`save(java.io.File file, + Chromosome chromosome, + Resources resources)` + Writes a chromosome into the specified .chr file. +

Modifier and Type	Method and Description
`Chromosome`	Population.`get(int index)` + Returns the indexed chromosome. +
`Chromosome`	Population.`getRandomChromosome()`

Modifier and Type	Method and Description
`boolean`	Chromosome.`compareActiveGenesTo(Chromosome chromosome)` + Does the same as `compareGenesto()` but only looks + at the active portion of the chromosome. +
`boolean`	Chromosome.`compareGenesTo(Chromosome chromosome)` + Performs a deep comparison between this chromosome and the provided one. +
`int`	Chromosome.`compareTo(Chromosome o)`
`void`	Chromosome.`copyGenes(Chromosome clone)` + Creates a deep copy of the specified chromosome in the + this instance. +

Modifier and Type	Class and Description
`class`	`Input` + This is a chromosome input. +
`class`	`Node` + Nodes make up the main part of the chromosome, + where the actual functions are evolved. +

Modifier and Type	Method and Description
`Connection`	Node.`getConnection(int index)`
`Connection`	Chromosome.`getRandomConnection()` + This method will pick a completely random connection, independently + of levels back, including inputs. +
`Connection`	Chromosome.`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. +
`Connection`	Output.`getSource()`

Modifier and Type	Method and Description
`void`	Node.`initialise(Function newFunction, + Connection... newConnections)` + Initialises the node with the specified values. +
`void`	Node.`setConnection(int index, + Connection newConnection)`
`void`	Output.`setConnection(int index, + Connection newConnection)` + When mutating an output, the index parameter + is simply ignored and the output source is + set. +
`void`	MutableElement.`setConnection(int index, + Connection newConnection)` + This method sets the indexed connection to the specified new connection. +

Modifier and Type	Method and Description
`Connection`	GUINode.`getChangingConnection()`
`Connection`	GUIInput.`getChangingConnection()`
`Connection`	GUIOutput.`getChangingConnection()`
`abstract Connection`	GUIGene.`getChangingConnection()`

Modifier and Type	Method and Description
`void`	GUINode.`setChangingConnection(Connection newConnection)`
`void`	GUIInput.`setChangingConnection(Connection newConnection)`
`void`	GUIOutput.`setChangingConnection(Connection newConnection)`
`abstract void`	GUIGene.`setChangingConnection(Connection newConnection)`

Modifier and Type	Method and Description
`boolean`	Node.`copyOf(MutableElement element)`
`boolean`	Output.`copyOf(MutableElement m)`
`boolean`	MutableElement.`copyOf(MutableElement element)` + Asserts if the specified element is a copy of the elements + this is called on. + This method returns true if and only if: + + the elements being compared are not the same instance; + the connections of the compared elements are not the same instance; + the elements have the same function (in the case of Node); + the grid position of the elements themselves are the same; + the grid position of all equivalent connections 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. + +

Modifier and Type	Method and Description
`void`	TournamentSelection.`evolve(Population population, + Mutator mutator)`
`abstract void`	EvolutionaryStrategy.`evolve(Population population, + Mutator mutator)` + Performs the selection algorithm and uses the mutator to create + the next generation of solutions. +
`void`	MuPlusLambda.`evolve(Population population, + Mutator mutator)`

Modifier and Type	Method and Description
`void`	SymbolicRegressionProblem.`evaluate(Population population, + Resources resources)`
`abstract void`	Problem.`evaluate(Population population, + Resources resources)` + The most important method of the problem type. +
`void`	DigitalCircuitProblem.`evaluate(Population population, + Resources resources)`
`int`	SymbolicRegressionProblem.`hasImprovement(Population population)`
`abstract int`	Problem.`hasImprovement(Population population)` + Used to assert whether a given population has a chromosome that is an improvement over + the current best chromosome. +
`int`	DigitalCircuitProblem.`hasImprovement(Population population)`
`int`	SymbolicRegressionProblem.`perfectSolutionFound(Population population)`
`abstract int`	Problem.`perfectSolutionFound(Population population)` + Used to assert whether a given population contains a perfect solution + to the problem. +
`int`	DigitalCircuitProblem.`perfectSolutionFound(Population population)`

Interface	Description
Connection	+ `Connection` declares the expected behaviour of any + part of a chromosome that can be connected to, specifically + nodes or inputs. +
MutableElement	+ `MutableElement` declares the expected behaviour of any + part of a chromosome that is mutable, more specifically + nodes or outputs. +

Class	Description
Chromosome	+ This class encapsulates a CGP chromosome. +
Input	+ This is a chromosome input. +
Node	+ Nodes make up the main part of the chromosome, + where the actual functions are evolved. +
Output	+ This is a chromosome output. +
Population	+ This class primarily holds a collection of chromosomes. +

Package	Description
jcgp
jcgp.backend.modules.es
jcgp.backend.modules.mutator
jcgp.backend.modules.problem
jcgp.backend.parsers
jcgp.backend.population
jcgp.gui.population

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

getRandomMutableElement

getRandomConnection

getRandomConnection

recomputeActiveNodes

getActiveNodes

compareGenesTo

compareActiveGenesTo

printNodes

getResources

compareTo

Interface Connection

Method Summary

Method Detail

getValue

Class Gene

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Gene

Class Input

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Input

Method Detail

setValue

getIndex

getValue

toString

Interface MutableElement

Method Summary

Method Detail

setConnection

copyOf

Class Node

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Node

Method Detail

setFunction

initialise

getColumn

getRow

getFunction

getConnection

copyOf

getValue

setConnection

toString

Class Output

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Output

Method Detail

calculate

getIndex

getSource

getActiveNodes

Uses of Class
jcgp.backend.population.Chromosome

Uses of Interface
jcgp.backend.population.Connection

Uses of Class
jcgp.backend.population.Gene

Uses of Class
jcgp.backend.population.Input

Uses of Interface
jcgp.backend.population.MutableElement

Uses of Class
jcgp.backend.population.Node

Uses of Class
jcgp.backend.population.Output

Uses of Class
jcgp.backend.population.Population

Uses of Package
jcgp.backend.population