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

Example 26 with IIndividual

use of forestry.api.genetics.IIndividual in project Binnie by ForestryMC.

the class ManagerGenetics method loadAlleles.

private void loadAlleles() {
    this.invalidChromosomeTypes.clear();
    for (IBreedingSystem system : BREEDING_SYSTEMS.values()) {
        ISpeciesRoot root = system.getSpeciesRoot();
        Map<IChromosomeType, List<IAllele>> chromosomeMap = new LinkedHashMap<>();
        for (IChromosomeType chromosome : root.getKaryotype()) {
            TreeSet<IAllele> alleles = new TreeSet<>(new ComparatorAllele());
            for (IIndividual individual : root.getIndividualTemplates()) {
                IGenome genome = individual.getGenome();
                IAllele activeAllele = genome.getActiveAllele(chromosome);
                IAllele inactiveAllele = genome.getInactiveAllele(chromosome);
                if (chromosome.getAlleleClass().isInstance(activeAllele)) {
                    alleles.add(activeAllele);
                }
                if (!chromosome.getAlleleClass().isInstance(inactiveAllele)) {
                    continue;
                }
                alleles.add(inactiveAllele);
            }
            system.addExtraAlleles(chromosome, alleles);
            if (alleles.size() == 0) {
                this.invalidChromosomeTypes.add(chromosome);
            } else {
                final List<IAllele> alleleList = new ArrayList<>(alleles);
                chromosomeMap.put(chromosome, alleleList);
            }
        }
        this.chromosomeArray.put(root, chromosomeMap);
    }
}

Example 27 with IIndividual

use of forestry.api.genetics.IIndividual in project Binnie by ForestryMC.

the class ControlIndividualDisplay method getTooltip.

@Override
public void getTooltip(Tooltip tooltip, ITooltipFlag tooltipFlag) {
    ItemStack stack = getItemStack();
    if (stack.isEmpty()) {
        return;
    }
    IIndividual ind = AlleleManager.alleleRegistry.getIndividual(stack);
    if (ind == null) {
        return;
    }
    tooltip.add(ind.getGenome().getPrimary().getAlleleName());
}

Example 28 with IIndividual

use of forestry.api.genetics.IIndividual in project Binnie by ForestryMC.

the class Splicer method setGene.

public static void setGene(IGene gene, ItemStack target, boolean setPrimary, boolean setSecondary) {
    int chromosomeID = gene.getChromosome().ordinal();
    Class<? extends IAllele> cls = gene.getChromosome().getAlleleClass();
    if (!cls.isInstance(gene.getAllele())) {
        return;
    }
    NBTTagCompound targetTag = target.getTagCompound();
    NBTTagCompound mate = null;
    if (targetTag != null && targetTag.hasKey("Mate")) {
        mate = targetTag.getCompoundTag("Mate").copy();
    }
    ISpeciesRoot speciesRoot = AlleleManager.alleleRegistry.getSpeciesRoot(target);
    Preconditions.checkNotNull(speciesRoot);
    IIndividual original = speciesRoot.getMember(target);
    Preconditions.checkNotNull(original);
    IChromosome[] chromosomes = original.getGenome().getChromosomes();
    IAllele[] primaryAlleles = new IAllele[chromosomes.length];
    IAllele[] secondaryAlleles = new IAllele[chromosomes.length];
    for (int i = 0; i < chromosomes.length; i++) {
        IChromosome chromosome = chromosomes[i];
        if (i == chromosomeID && setPrimary) {
            primaryAlleles[i] = gene.getAllele();
        } else {
            primaryAlleles[i] = chromosome.getPrimaryAllele();
        }
        if (i == chromosomeID && setSecondary) {
            secondaryAlleles[i] = gene.getAllele();
        } else {
            secondaryAlleles[i] = chromosome.getSecondaryAllele();
        }
    }
    IIndividual individual = speciesRoot.templateAsIndividual(primaryAlleles, secondaryAlleles);
    if (original.isAnalyzed()) {
        individual.analyze();
    }
    if (original instanceof IBee) {
        IBee individualBee = (IBee) individual;
        IBee originalBee = (IBee) original;
        individualBee.setIsNatural(originalBee.isNatural());
    }
    NBTTagCompound nbt = new NBTTagCompound();
    individual.writeToNBT(nbt);
    if (mate != null) {
        nbt.setTag("Mate", mate);
    }
    target.setTagCompound(nbt);
}

Example 29 with IIndividual

use of forestry.api.genetics.IIndividual in project Binnie by ForestryMC.

the class SplicerLogic method isValidSerum.

@Nullable
public ErrorState isValidSerum() {
    final ItemStack serum = this.getUtil().getStack(Splicer.SLOT_SERUM_VIAL);
    if (serum.isEmpty()) {
        return null;
    }
    final ItemStack target = this.getUtil().getStack(Splicer.SLOT_TARGET);
    final IGene[] genes = Engineering.getGenes(serum);
    if (genes.length == 0) {
        return new ErrorState(GeneticsErrorCode.INVALID_SERUM_NO);
    }
    if (!genes[0].getSpeciesRoot().isMember(target)) {
        return new ErrorState(GeneticsErrorCode.INVALID_SERUM_MISMATCH);
    }
    final IIndividual individual = genes[0].getSpeciesRoot().getMember(target);
    boolean hasAll = true;
    for (final IGene gene : genes) {
        if (hasAll) {
            final IAllele a = individual.getGenome().getActiveAllele(gene.getChromosome());
            final IAllele b = individual.getGenome().getInactiveAllele(gene.getChromosome());
            hasAll = (hasAll && a.getUID().equals(gene.getAllele().getUID()) && b.getUID().equals(gene.getAllele().getUID()));
        }
    }
    if (hasAll) {
        return new ErrorState(GeneticsErrorCode.DEFUNCT_SERUM);
    }
    return null;
}

Example 30 with IIndividual

use of forestry.api.genetics.IIndividual in project Binnie by ForestryMC.

the class SplicerLogic method getGenesToUse.

public static int getGenesToUse(ItemStack serum, ItemStack target) {
    if (serum.isEmpty() || target.isEmpty()) {
        return 1;
    }
    final IIndividual ind = AlleleManager.alleleRegistry.getIndividual(target);
    final IGene[] genes = ((IItemSerum) serum.getItem()).getGenes(serum);
    if (ind.getGenome().getSpeciesRoot() != ((IItemSerum) serum.getItem()).getSpeciesRoot(serum)) {
        return 1;
    }
    int i = 0;
    for (final IGene gene : genes) {
        if (ind.getGenome().getActiveAllele(gene.getChromosome()) != gene.getAllele() || ind.getGenome().getInactiveAllele(gene.getChromosome()) != gene.getAllele()) {
            ++i;
        }
    }
    return (i < 1) ? 1 : i;
}