Examples with IChromosome forestry.api.genetics.IChromosome used on opensource projects

Example 1 with IChromosome

use of forestry.api.genetics.IChromosome in project ForestryMC by ForestryMC.

the class TreeGenome method calculateMatchesTemplateGenome.

private boolean calculateMatchesTemplateGenome() {
    IAlleleTreeSpecies primary = getPrimary();
    IAllele[] template = getSpeciesRoot().getTemplate(primary);
    IChromosome[] chromosomes = getChromosomes();
    for (int i = 0; i < chromosomes.length; i++) {
        IChromosome chromosome = chromosomes[i];
        String templateUid = template[i].getUID();
        IAllele primaryAllele = chromosome.getPrimaryAllele();
        if (!primaryAllele.getUID().equals(templateUid)) {
            return false;
        }
        IAllele secondaryAllele = chromosome.getSecondaryAllele();
        if (!secondaryAllele.getUID().equals(templateUid)) {
            return false;
        }
    }
    return true;
}

Example 2 with IChromosome

use of forestry.api.genetics.IChromosome in project ForestryMC by ForestryMC.

the class Genome method getChromosomes.

private static IChromosome[] getChromosomes(NBTTagCompound genomeNBT, ISpeciesRoot speciesRoot) {
    NBTTagList chromosomesNBT = genomeNBT.getTagList("Chromosomes", 10);
    IChromosome[] chromosomes = new IChromosome[speciesRoot.getDefaultTemplate().length];
    String primarySpeciesUid = null;
    String secondarySpeciesUid = null;
    for (int i = 0; i < chromosomesNBT.tagCount(); i++) {
        NBTTagCompound chromosomeNBT = chromosomesNBT.getCompoundTagAt(i);
        byte chromosomeOrdinal = chromosomeNBT.getByte(SLOT_TAG);
        if (chromosomeOrdinal >= 0 && chromosomeOrdinal < chromosomes.length) {
            IChromosomeType chromosomeType = speciesRoot.getKaryotype()[chromosomeOrdinal];
            Chromosome chromosome = Chromosome.create(primarySpeciesUid, secondarySpeciesUid, chromosomeType, chromosomeNBT);
            chromosomes[chromosomeOrdinal] = chromosome;
            if (chromosomeOrdinal == speciesRoot.getSpeciesChromosomeType().ordinal()) {
                primarySpeciesUid = chromosome.getPrimaryAllele().getUID();
                secondarySpeciesUid = chromosome.getSecondaryAllele().getUID();
            }
        }
    }
    return chromosomes;
}

Example 3 with IChromosome

use of forestry.api.genetics.IChromosome in project ForestryMC by ForestryMC.

the class Genome method checkChromosomes.

private void checkChromosomes(IChromosome[] chromosomes) {
    if (chromosomes.length != getDefaultTemplate().length) {
        String message = String.format("Tried to create a genome for '%s' from an invalid chromosome template.\n%s", getSpeciesRoot().getUID(), chromosomesToString(chromosomes));
        throw new IllegalArgumentException(message);
    }
    IChromosomeType[] karyotype = getSpeciesRoot().getKaryotype();
    for (int i = 0; i < karyotype.length; i++) {
        IChromosomeType chromosomeType = karyotype[i];
        IChromosome chromosome = chromosomes[i];
        if (chromosome == null) {
            String message = String.format("Tried to create a genome for '%s' from an invalid chromosome template. " + "Missing chromosome '%s'.\n%s", getSpeciesRoot().getUID(), chromosomeType.getName(), chromosomesToString(chromosomes));
            throw new IllegalArgumentException(message);
        }
        IAllele primary = chromosome.getPrimaryAllele();
        if (primary == null) {
            String message = String.format("Tried to create a genome for '%s' from an invalid chromosome template. " + "Missing primary allele for '%s'.\n%s", getSpeciesRoot().getUID(), chromosomeType.getName(), chromosomesToString(chromosomes));
            throw new IllegalArgumentException(message);
        }
        IAllele secondary = chromosome.getSecondaryAllele();
        if (secondary == null) {
            String message = String.format("Tried to create a genome for '%s' from an invalid chromosome template. " + "Missing secondary allele for '%s'.\n%s", getSpeciesRoot().getUID(), chromosomeType.getName(), chromosomesToString(chromosomes));
            throw new IllegalArgumentException(message);
        }
        Class<? extends IAllele> chromosomeAlleleClass = chromosomeType.getAlleleClass();
        if (!chromosomeAlleleClass.isAssignableFrom(primary.getClass())) {
            String message = String.format("Tried to create a genome for '%s' from an invalid chromosome template. " + "Incorrect type for primary allele '%s'.\n%s.", getSpeciesRoot().getUID(), chromosomeType.getName(), chromosomesToString(chromosomes));
            throw new IllegalArgumentException(message);
        }
        if (!chromosomeAlleleClass.isAssignableFrom(secondary.getClass())) {
            String message = String.format("Tried to create a genome for '%s' from an invalid chromosome template. " + "Incorrect type for secondary allele '%s'.\n%s.", getSpeciesRoot().getUID(), chromosomeType.getName(), chromosomesToString(chromosomes));
            throw new IllegalArgumentException(message);
        }
    }
}

Example 4 with IChromosome

use of forestry.api.genetics.IChromosome in project ForestryMC by ForestryMC.

the class Genome method isGeneticEqual.

@Override
public boolean isGeneticEqual(IGenome other) {
    IChromosome[] genetics = other.getChromosomes();
    if (chromosomes.length != genetics.length) {
        return false;
    }
    for (int i = 0; i < chromosomes.length; i++) {
        IChromosome chromosome = chromosomes[i];
        IChromosome otherChromosome = genetics[i];
        if (chromosome == null && otherChromosome == null) {
            continue;
        }
        if (chromosome == null || otherChromosome == null) {
            return false;
        }
        if (!chromosome.getPrimaryAllele().getUID().equals(otherChromosome.getPrimaryAllele().getUID())) {
            return false;
        }
        if (!chromosome.getSecondaryAllele().getUID().equals(otherChromosome.getSecondaryAllele().getUID())) {
            return false;
        }
    }
    return true;
}

Example 5 with IChromosome

use of forestry.api.genetics.IChromosome in project ForestryMC by ForestryMC.

the class Butterfly method mutateSpecies.

@Nullable
private static IChromosome[] mutateSpecies(World world, IButterflyNursery nursery, IGenome genomeOne, IGenome genomeTwo) {
    IChromosome[] parent1 = genomeOne.getChromosomes();
    IChromosome[] parent2 = genomeTwo.getChromosomes();
    IGenome genome0;
    IGenome genome1;
    IAllele allele0;
    IAllele allele1;
    if (rand.nextBoolean()) {
        allele0 = parent1[EnumButterflyChromosome.SPECIES.ordinal()].getPrimaryAllele();
        allele1 = parent2[EnumButterflyChromosome.SPECIES.ordinal()].getSecondaryAllele();
        genome0 = genomeOne;
        genome1 = genomeTwo;
    } else {
        allele0 = parent2[EnumButterflyChromosome.SPECIES.ordinal()].getPrimaryAllele();
        allele1 = parent1[EnumButterflyChromosome.SPECIES.ordinal()].getSecondaryAllele();
        genome0 = genomeTwo;
        genome1 = genomeOne;
    }
    for (IButterflyMutation mutation : ButterflyManager.butterflyRoot.getMutations(true)) {
        float chance = mutation.getChance(world, nursery, allele0, allele1, genome0, genome1);
        if (chance > rand.nextFloat() * 100) {
            return ButterflyManager.butterflyRoot.templateAsChromosomes(mutation.getTemplate());
        }
    }
    return null;
}