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Move creation of DNA to Gene Pool
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This is long overdue, and it fixes all the problems with the damn DNA
serial ids and the horrible mechanics of their creation and updating.
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@nusco
nusco committed Feb 22, 2015
1 parent 926a3ee commit 90e3290
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Showing 24 changed files with 151 additions and 305 deletions.
3 changes: 2 additions & 1 deletion narjillos-core/src/main/java/org/nusco/narjillos/creature/Egg.java
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Expand Up @@ -13,7 +13,8 @@
public class Egg implements Thing {

public static final double RADIUS = 25;

public static final int INCUBATION_TIME = 500;

private final DNA dna;
private int age = 0;
private Vector position;
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12 changes: 0 additions & 12 deletions narjillos-core/src/main/java/org/nusco/narjillos/creature/Narjillo.java
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Expand Up @@ -11,15 +11,13 @@
import org.nusco.narjillos.shared.things.Energy;
import org.nusco.narjillos.shared.things.FoodPiece;
import org.nusco.narjillos.shared.things.Thing;
import org.nusco.narjillos.shared.utilities.RanGen;

/**
* A fully-formed, autonomous creature.
*/
public class Narjillo implements Thing {

static final double MAX_LIFESPAN = 30_000;
private static final int INCUBATION_TIME = 500;

private final Body body;
private final DNA dna;
Expand Down Expand Up @@ -73,16 +71,6 @@ public void feedOn(FoodPiece thing) {
thing.setEater(this);
}

public Egg layEgg(Vector position, RanGen ranGen) {
double percentEnergyToChildren = body.getPercentEnergyToChildren();
double childEnergy = energy.chunkOff(percentEnergyToChildren);
if (childEnergy == 0)
return null;

DNA childDNA = getDNA().copyWithMutations(ranGen);
return new Egg(childDNA, getPosition(), childEnergy, INCUBATION_TIME);
}

@Override
public String getLabel() {
return "narjillo";
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36 changes: 21 additions & 15 deletions narjillos-core/src/main/java/org/nusco/narjillos/ecosystem/Ecosystem.java
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Expand Up @@ -17,6 +17,7 @@
import org.nusco.narjillos.creature.Egg;
import org.nusco.narjillos.creature.Narjillo;
import org.nusco.narjillos.genomics.DNA;
import org.nusco.narjillos.genomics.GenePool;
import org.nusco.narjillos.shared.physics.Segment;
import org.nusco.narjillos.shared.physics.Vector;
import org.nusco.narjillos.shared.things.FoodPiece;
Expand Down Expand Up @@ -75,15 +76,15 @@ public Vector findClosestFoodPiece(Thing thing) {
return target.getPosition();
}

public void tick(RanGen ranGen) {
public void tick(GenePool genePool, RanGen ranGen) {
for (Thing thing : new LinkedList<>(things.getAll("egg")))
tickEgg((Egg) thing);

for (Narjillo narjillo : new LinkedList<>(narjillos))
if (narjillo.isDead())
removeNarjillo(narjillo);
removeNarjillo(narjillo, genePool);

tickNarjillos(ranGen);
tickNarjillos(genePool, ranGen);

if (shouldSpawnFood(ranGen)) {
spawnFood(randomPosition(getSize(), ranGen));
Expand Down Expand Up @@ -153,7 +154,7 @@ private void tickEgg(Egg egg) {
remove(egg);
}

private synchronized void tickNarjillos(RanGen ranGen) {
private synchronized void tickNarjillos(GenePool genePool, RanGen ranGen) {
if (executorService.isShutdown())
return; // we're leaving, apparently

Expand All @@ -165,7 +166,7 @@ private synchronized void tickNarjillos(RanGen ranGen) {
for (Entry<Narjillo, Set<Thing>> entry : narjillosToCollidedFood.entrySet()) {
Narjillo narjillo = entry.getKey();
Set<Thing> collidedFood = entry.getValue();
consume(narjillo, collidedFood, ranGen);
consume(narjillo, collidedFood, genePool, ranGen);
}
}

Expand Down Expand Up @@ -225,20 +226,20 @@ private void updateTargets(Thing food) {
}
}

private void consume(Narjillo narjillo, Set<Thing> foodPieces, RanGen ranGen) {
private void consume(Narjillo narjillo, Set<Thing> foodPieces, GenePool genePool, RanGen ranGen) {
for (Thing foodPiece : foodPieces)
consumeFood(narjillo, (FoodPiece) foodPiece, ranGen);
consumeFood(narjillo, (FoodPiece) foodPiece, genePool, ranGen);
}

private void consumeFood(Narjillo narjillo, FoodPiece foodPiece, RanGen ranGen) {
private void consumeFood(Narjillo narjillo, FoodPiece foodPiece, GenePool genePool, RanGen ranGen) {
if (!things.contains(foodPiece))
return; // race condition: already consumed

remove(foodPiece);

narjillo.feedOn(foodPiece);

layEgg(narjillo, ranGen);
layEgg(narjillo, genePool, ranGen);
updateTargets(foodPiece);
}

Expand All @@ -247,16 +248,21 @@ private void remove(Thing thing) {
things.remove(thing);
}

private void removeNarjillo(Narjillo narjillo) {
private void removeNarjillo(Narjillo narjillo, GenePool genePool) {
notifyThingRemoved(narjillo);
narjillos.remove(narjillo);
narjillo.getDNA().destroy();
genePool.remove(narjillo.getDNA());
}

private void layEgg(Narjillo narjillo, RanGen ranGen) {
Egg egg = narjillo.layEgg(narjillo.getNeckLocation(), ranGen);
if (egg == null) // refused to lay egg
return;
private void layEgg(Narjillo narjillo, GenePool genePool, RanGen ranGen) {
double percentEnergyToChildren = narjillo.getBody().getPercentEnergyToChildren();
double childEnergy = narjillo.getEnergy().chunkOff(percentEnergyToChildren);
if (childEnergy == 0)
return; // refused to lay egg
DNA childDNA = genePool.mutateDNA(narjillo.getDNA(), ranGen);

Vector position = narjillo.getNeckLocation();
Egg egg = new Egg(childDNA, position, childEnergy, Egg.INCUBATION_TIME);
insert(egg);
}

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15 changes: 3 additions & 12 deletions narjillos-core/src/main/java/org/nusco/narjillos/experiment/Experiment.java
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Expand Up @@ -2,7 +2,6 @@

import org.nusco.narjillos.creature.body.physics.Viscosity;
import org.nusco.narjillos.ecosystem.Ecosystem;
import org.nusco.narjillos.genomics.DNA;
import org.nusco.narjillos.genomics.GenePool;
import org.nusco.narjillos.shared.physics.Vector;
import org.nusco.narjillos.shared.utilities.Chronometer;
Expand Down Expand Up @@ -47,7 +46,6 @@ private void initializeGenePool(boolean trackGenePool) {
return;

genePool.enableTracking();
DNA.setObserver(genePool);
}

public final void timeStamp() {
Expand All @@ -64,10 +62,10 @@ private void populate(Ecosystem ecosystem, String dna) {

if (dna == null) {
for (int i = 0; i < INITIAL_NUMBER_OF_NARJILLOS; i++)
ecosystem.spawnEgg(DNA.random(ranGen), randomPosition(ecosystem.getSize()), ranGen);
ecosystem.spawnEgg(getGenePool().createRandomDNA(ranGen), randomPosition(ecosystem.getSize()), ranGen);
} else {
for (int i = 0; i < INITIAL_NUMBER_OF_NARJILLOS; i++)
ecosystem.spawnEgg(new DNA(dna), randomPosition(ecosystem.getSize()), ranGen);
ecosystem.spawnEgg(getGenePool().createDNA(dna), randomPosition(ecosystem.getSize()), ranGen);
}
}

Expand All @@ -79,7 +77,7 @@ public boolean tick() {
if (ticksChronometer.getTotalTicks() % 1000 == 0)
executePeriodicOperations();

getEcosystem().tick(ranGen);
getEcosystem().tick(genePool, ranGen);
ticksChronometer.tick();
return areThereSurvivors();
}
Expand Down Expand Up @@ -127,13 +125,6 @@ public GenePool getGenePool() {
return genePool;
}

// For serialization only. Don't call this in other situations, if you don't
// want to make the experiment non-deterministic.
public void setGenePool(GenePool genePool) {
this.genePool = genePool;
DNA.setObserver(genePool);
}

@Override
public String toString() {
return "Experiment " + getId();
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70 changes: 11 additions & 59 deletions narjillos-core/src/main/java/org/nusco/narjillos/genomics/DNA.java
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Expand Up @@ -12,44 +12,18 @@ public class DNA {

public static final double MUTATION_RATE = 0.055;
private static final int GENE_MUTATION_RANGE = 15;
private static DNAObserver observer = DNAObserver.NULL;

// TODO: This static makes testing difficult. Find another way.
private static long serial = 0;

// for testing
public static long getSerial() {
return serial;
}

public static void setSerial(long value) {
serial = value;
}

private long id;
private final long id;

private final Integer[] genes;

public DNA(String dnaDocument) {
this(new DNADocument(dnaDocument).toGenes());
}

// Only use for deserialization.
public DNA(String dnaDocument, long id) {
public DNA(long id, String dnaDocument) {
this.id = id;
this.genes = clipGenes(new DNADocument(dnaDocument).toGenes());
setId(id);
}

private DNA(Integer... genes) {
this.genes = clipGenes(genes);
setId(serial + 1);
DNA.observer.created(this, null);
}

private DNA(DNA parent, Integer... genes) {
public DNA(long id, Integer[] genes) {
this.id = id;
this.genes = clipGenes(genes);
setId(serial + 1);
DNA.observer.created(this, parent);
}

public long getId() {
Expand All @@ -60,11 +34,7 @@ public Integer[] getGenes() {
return genes;
}

public void destroy() {
DNA.observer.removed(this);
}

public DNA copyWithMutations(RanGen ranGen) {
public DNA copyWithMutations(long id, RanGen ranGen) {
List<Integer[]> resultChromosomes = new LinkedList<>();

DNAIterator iterator = new DNAIterator(this);
Expand All @@ -79,12 +49,12 @@ public DNA copyWithMutations(RanGen ranGen) {
}

Integer[] resultGenes = flatten(resultChromosomes);
return new DNA(this, resultGenes);
return new DNA(id, resultGenes);
}

public static DNA random(RanGen ranGen) {
public static DNA random(long id, RanGen ranGen) {
int size = Chromosome.SIZE * (Math.abs(ranGen.nextInt()) % 10 + 2);
return random(size, ranGen);
return random(id, ranGen, size);
}

// From: http://en.wikipedia.org/wiki/Levenshtein_distance,
Expand Down Expand Up @@ -129,10 +99,6 @@ public int getLevenshteinDistanceFrom(DNA other) {
return v1[otherGenes.length];
}

public static void setObserver(DNAObserver dnaObserver) {
DNA.observer = dnaObserver;
}

@Override
public int hashCode() {
return (int) getId();
Expand All @@ -153,20 +119,6 @@ private Integer[] clipGenes(Integer[] genes) {
return (genes.length > 0) ? clipToByteSize(genes) : new Integer[] { 0 };
}

private void setId(long id) {
this.id = id;
// This complicated mechanism guarantees that even
// after deserializing DNA, the serial will still
// contain the highest id in the system. (But
// if you generate DNA and *then* deserialize
// other DNA, then you might have duplicated
// DNA ids in the system. I assume that you
// will only deserialize DNA before ever creating
// it.
if (id > serial)
serial = id;
}

private Integer[] copyWithMutations(Chromosome chromosome, RanGen ranGen) {
Integer[] result = new Integer[Chromosome.SIZE];
for (int i = 0; i < result.length; i++)
Expand Down Expand Up @@ -210,9 +162,9 @@ private int clipToByteSize(int number) {
return Math.max(0, Math.min(255, number));
}

private static DNA random(int size, RanGen ranGen) {
private static DNA random(long id, RanGen ranGen, int size) {
Integer[] genes = randomGenes(size, ranGen);
return new DNA(genes);
return new DNA(id, genes);
}

private static Integer[] randomGenes(int size, RanGen ranGen) {
Expand Down
21 changes: 0 additions & 21 deletions narjillos-core/src/main/java/org/nusco/narjillos/genomics/DNAObserver.java
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