genetics

type ByOrganismFitness []*Species

type EpochExecutorType int

type Gene struct {
	// The link between nodes
	Link *network.Link
	// The current innovation number for this gene
	InnovationNum int64
	// Used to see how much mutation has changed the link
	MutationNum float64
	// If true the gene is enabled
	IsEnabled bool
}

type Genome struct {
	// The genome ID
	Id int
	// The parameters conglomerations
	Traits []*neat.Trait
	// List of NNodes for the Network
	Nodes []*network.NNode
	// List of innovation-tracking genes
	Genes []*Gene
	// List of MIMO control genes
	ControlGenes []*MIMOControlGene

	// Allows Genome to be matched with its Network
	Phenotype *network.Network
}

type GenomeEncoding byte

type GenomeReader interface {
	// Reads one Genome record
	Read() (*Genome, error)
}

type GenomeWriter interface {
	// Writes Genome record
	WriteGenome(genome *Genome) error
}

type Innovation struct {

	// Two nodes specify where the innovation took place
	InNodeId  int
	OutNodeId int
	// The number assigned to the innovation
	InnovationNum int64
	// If this is a new node innovation, then there are 2 innovations (links) added for the new node
	InnovationNum2 int64

	// If a link is added, this is its weight
	NewWeight float64
	// If a link is added, this is its connected trait index
	NewTraitNum int
	// If a new node was created, this is its node_id
	NewNodeId int

	// If a new node was created, this is the innovation number of the gene's link it is being stuck inside
	OldInnovNum int64

	// Flag to indicate whether its innovation for recurrent link
	IsRecurrent bool
	// contains filtered or unexported fields
}

type MIMOControlGene struct {
	// The current innovation number for this gene
	InnovationNum int64
	// Used to see how much mutation has changed the link
	MutationNum float64
	// If true the gene is enabled
	IsEnabled bool

	// The control node with control/activation function
	ControlNode *network.NNode
	// contains filtered or unexported fields
}

type Organism struct {
	// A measure of fitness for the Organism
	Fitness float64
	// The error value indicating how far organism's performance is from ideal task goal, e.g. MSE
	Error float64
	// Win marker (if needed for a particular task)
	IsWinner bool

	// The Organism's phenotype
	Phenotype *network.Network
	// The Organism's genotype
	Genotype *Genome
	// The Species of the Organism
	Species *Species

	// Number of children this Organism may have
	ExpectedOffspring float64
	// Tells which generation this Organism is from
	Generation int

	// The utility data transfer object to be used by different GA implementations to hold additional data.
	// Implemented as ANY to allow implementation specific objects.
	Data *OrganismData

	// The flag to be used as utility value
	Flag int
	// contains filtered or unexported fields
}

type OrganismData struct {
	// The implementation specific data object to be associated with organism
	Value interface{}
}

type Organisms []*Organism

type ParallelPopulationEpochExecutor struct {
	// contains filtered or unexported fields
}

type Population struct {
	// Species in the Population. Note that the species should comprise all the genomes
	Species []*Species
	// The organisms in the Population
	Organisms []*Organism
	// The highest species number
	LastSpecies int
	// For holding the genetic innovations of the newest generation
	Innovations []*Innovation
	// An integer that when above zero tells when the first winner appeared
	WinnerGen int
	// The last generation played
	FinalGen int

	// Stagnation detector
	HighestFitness float64
	// The number of epochs when highest fitness was recorded for this population. If it was too long before
	// than delta coding will be applied to avoid population's fitness stagnation
	EpochsHighestLastChanged int

	/* Fitness Statistics */
	MeanFitness float64
	Variance    float64
	StandardDev float64
	// contains filtered or unexported fields
}

type PopulationEpochExecutor interface {
	// Turnover the population to a new generation
	NextEpoch(generation int, population *Population, context *neat.NeatContext) error
}

type SequentialPopulationEpochExecutor struct {
	// contains filtered or unexported fields
}

type Species struct {
	// The ID
	Id int
	// The age of the Species
	Age int
	// The maximal fitness it ever had
	MaxFitnessEver float64
	// How many child expected
	ExpectedOffspring int

	// Is it novel
	IsNovel bool

	// The organisms in the Species
	Organisms Organisms
	// If this is too long ago, the Species will goes extinct
	AgeOfLastImprovement int

	// Flag used for search optimization
	IsChecked bool
}