A C D E F G M O P S T V

A

actionPerformed(ActionEvent) - Method in class FoldingApp

The method extract the user input, chain.getText(), calls Folding.solve to obtain a solution, which is then pass to the FoldPanel fp

C

Chromosome - Class in <Unnamed>

Chromosome(String) - Constructor for class Chromosome

A constructor that initializes this chromosome with random moves for this chain.

Chromosome(Chromosome) - Constructor for class Chromosome

A constructor that initializes the content of this Chromosome with that of other.

crossOver(Chromosome) - Method in class Chromosome

With probability CROSSOVER_RATE the method returns a new Chromosome consisting of a certain number of contiguous genes from this solution and the rest of the genes coming from other.

CROSSOVER_RATE - Static variable in class Chromosome

A constant that specifies the cross over rate (see crossover).

D

DEFAULT_CHAIN - Static variable in class Folding

The chain that will be used if no argument was supplied on the command line.

DEFAULT_POPULATION_SIZE - Static variable in class Population

A constant that will be used as the default size of the population

display() - Static method in class StudentInfo

Displays the student information: student name, id, section, etc.

E

evolve() - Method in class Population

The method evolve selects parent chromosomes.

F

Folding - Class in <Unnamed>

The class Folding implements the top level of the algorithm.

Folding() - Constructor for class Folding

FoldingApp - Class in <Unnamed>

FoldingApp() - Constructor for class FoldingApp

The constructor creates the layout of the application.

FoldPanel - Class in <Unnamed>

FoldPanel() - Constructor for class FoldPanel

G

getChain() - Method in class Chromosome

Returns the chain of constitents of this chromosome.

getFitness() - Method in class Chromosome

Returns an integer value that reflects the quality of the solution.

getFittest() - Method in class Population

The instance method public Chromosome getFittest() returns the "best" individual of the population, i.e.

getGene(int) - Method in class Chromosome

Returns the value of the gene at the given position of the chromosome.

M

main(String[]) - Static method in class Folding

The main method of this program.

main(String[]) - Static method in class FoldingApp

Launches the application.

MAX_GENERATIONS - Static variable in class Folding

A constant that specifies the maximum number of generations (iterations) for a run.

Move - Enum in <Unnamed>

An enumerative type that defines legal moves on a two-dimensional grid.

moves - Static variable in enum Move

Caching the array to avoid regenerating it several times

mutate() - Method in class Chromosome

Applies mutations to this chromosome.

MUTATION_RATE - Static variable in class Chromosome

A constant that specifies the mutation rate (see mutate).

O

OVERLAP_PENALTY - Static variable in class Chromosome

A penalty that will be applied for each overlapping constituent.

P

paintComponent(Graphics) - Method in class FoldPanel

Called every time the surface needs to be repainted.

Population - Class in <Unnamed>

Population(int, String) - Constructor for class Population

A constructor of arity 2 to initialize the Population.

Population(String) - Constructor for class Population

A constructor of arity 1 to initialize the Population.

S

setSolution(Chromosome) - Method in class FoldPanel

A setter method.

size() - Method in class Chromosome

Returns the size of this chromosome, which is the number of genes.

solve(String) - Static method in class Folding

Implements the top loop of the genetic algorithm.

StudentInfo - Class in <Unnamed>

StudentInfo() - Constructor for class StudentInfo

T

toString() - Method in class Chromosome

Returns a String representation of this Chromosome.

toString() - Method in class Population

Returns a String representation of this Population.

V

valueOf(String) - Static method in enum Move

Returns the enum constant of this type with the specified name.

values() - Static method in enum Move

Returns an array containing the constants of this enum type, in the order they are declared.

A C D E F G M O P S T V