Make Escritoire give unlearned mutation notes first

(no fix for vanilla leaves, the harvest event is fired server-side only)

build.gradle

@@ -40,7 +40,6 @@ targetCompatibility = 1.8
 minecraft {
 	version = mcversion + "-" + forgeversion
 	runDir = "run"
-	useDepAts = true
 	mappings = mcp_mappings
 
 	replace '@VERSION@', project.version
@@ -66,7 +65,8 @@ repositories {
 }
 
 dependencies {
-	deobfCompile "mezz.jei:jei_${mcversion}:${jei_version}"
+	deobfCompile "mezz.jei:jei_${mcversion}:${jei_version}:api"
+	runtime "mezz.jei:jei_${mcversion}:${jei_version}"
 	deobfCompile "net.industrial-craft:industrialcraft-2:${ic2_version}:api"
 }
 

gradle.properties

@@ -1,10 +1,10 @@
-mcversion=1.9.4
-forgeversion=12.17.0.1968
+mcversion=1.10
+forgeversion=12.18.0.1989-1.10.0
 mcp_mappings=snapshot_20160525
 
-jei_version=3.6.4.+
+jei_version=3.7.0.+
 ic2_version=2.5.5-ex19
 
 version_major=5
-version_minor=0
-version_patch=23
+version_minor=1
+version_patch=6

src/main/java/forestry/Forestry.java

@@ -49,16 +49,9 @@ import forestry.plugins.PluginManager;
 		name = "Forestry",
 		version = Constants.VERSION,
 		guiFactory = "forestry.core.config.ForestryGuiConfigFactory",
-		dependencies = "required-after:Forge@[12.17.0.1963,);"
-				+ "after:Buildcraft|Core@[7.2,);"
-				+ "after:BuildCraft|Energy@[7.2,);"
-				+ "after:ExtrabiomesXL;"
-				+ "after:BiomesOPlenty;"
-				+ "after:IC2@[2.3.235,);"
-				+ "after:Natura@[2.2.0,);"
-				+ "after:HardcoreEnderExpansion;"
-				+ "after:JEI@[3.6.4,);"
-				+ "after:basemetals;")
+		acceptedMinecraftVersions = "[1.10]",
+		dependencies = "required-after:Forge@[12.18.0.1989,);"
+				+ "after:JEI@[3.7.0,);")
 public class Forestry {
 
 	@Mod.Instance(Constants.MOD_ID)

src/main/java/forestry/api/apiculture/IBeeRoot.java

@@ -7,17 +7,15 @@ package forestry.api.apiculture;
 
 import javax.annotation.Nullable;
 import java.util.ArrayList;
-import java.util.Collection;
+import java.util.List;
 
+import com.mojang.authlib.GameProfile;
+import forestry.api.genetics.IAllele;
+import forestry.api.genetics.ISpeciesRoot;
 import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.world.World;
 
-import com.mojang.authlib.GameProfile;
-
-import forestry.api.genetics.IAllele;
-import forestry.api.genetics.ISpeciesRoot;
-
 public interface IBeeRoot extends ISpeciesRoot {
 
 	/**
@@ -100,7 +98,7 @@ public interface IBeeRoot extends ISpeciesRoot {
 
 	/* MUTATIONS */
 	@Override
-	Collection<IBeeMutation> getMutations(boolean shuffle);
+	List<IBeeMutation> getMutations(boolean shuffle);
 
 	/* GAME MODE */
 	void resetBeekeepingMode();

src/main/java/forestry/api/apiculture/IJubilanceFactory.java

@@ -5,12 +5,12 @@
  ******************************************************************************/
 package forestry.api.apiculture;
 
-import net.minecraft.block.Block;
+import net.minecraft.block.state.IBlockState;
 
 public interface IJubilanceFactory {
 	/** The default Jubilance Provider is satisfied when the humidity and temperature are ideal for the bee. */
 	IJubilanceProvider getDefault();
 
 	/** The Requires Resource Jubilance Provider is satisfied when a specific block is under the hive. */
-	IJubilanceProvider getRequiresResource(Block block, int meta);
+	IJubilanceProvider getRequiresResource(IBlockState... acceptedBlockStates);
 }

src/main/java/forestry/api/arboriculture/EnumForestryWoodType.java

@@ -10,28 +10,53 @@ import java.util.Locale;
 import java.util.Random;
 
 public enum EnumForestryWoodType implements IWoodType {
-	LARCH, TEAK, ACACIA, LIME,
-	CHESTNUT, WENGE, BAOBAB, SEQUOIA(4.0f),
+	LARCH(4, 20),
+	TEAK(4, 20),
+	ACACIA(4, 20),
+	LIME(4, 19),
+	CHESTNUT(4, 21),
+	WENGE(4, 20),
+	BAOBAB(4, 20),
+	SEQUOIA(3, 18, 4.0f),
 
-	KAPOK, EBONY, MAHOGANY, BALSA(1.0f),
-	WILLOW, WALNUT, GREENHEART(7.5f), CHERRY,
+	KAPOK(4, 20),
+	EBONY(4, 20),
+	MAHOGANY(4, 20),
+	BALSA(4, 20, 1.0f),
+	WILLOW(4, 20),
+	WALNUT(4, 21),
+	GREENHEART(4, 20, 7.5f),
+	CHERRY(4, 20),
 
-	MAHOE, POPLAR, PALM, PAPAYA,
-	PINE(3.0f), PLUM, MAPLE, CITRUS,
+	MAHOE(4, 20),
+	POPLAR(4, 20),
+	PALM(4, 20),
+	PAPAYA(4, 20),
+	PINE(4, 20, 3.0f),
+	PLUM(4, 20),
+	MAPLE(4, 20),
+	CITRUS(4, 20),
 
-	GIGANTEUM, IPE, PADAUK, COCOBOLO,
-	ZEBRAWOOD;
+	GIGANTEUM(3, 18, 4.0f),
+	IPE(4, 20),
+	PADAUK(4, 20),
+	COCOBOLO(4, 20),
+	ZEBRAWOOD(4, 20);
 
 	public static final float DEFAULT_HARDNESS = 2.0f;
 	public static final EnumForestryWoodType[] VALUES = values();
 
+	private final int carbonization;
+	private final int combustability;
 	private final float hardness;
 
-	EnumForestryWoodType() {
-		this(DEFAULT_HARDNESS);
+	EnumForestryWoodType(int carbonization, int combustability) {
+		this(carbonization, combustability, DEFAULT_HARDNESS);
 	}
 
-	EnumForestryWoodType(float hardness) {
+	EnumForestryWoodType(int carbonization, int combustability, float hardness) {
+		this.carbonization = carbonization;
+		this.combustability = combustability;
 		this.hardness = hardness;
 	}
 
@@ -66,4 +91,12 @@ public enum EnumForestryWoodType implements IWoodType {
 		}
 		return VALUES[meta];
 	}
+
+	public int getCarbonization() {
+		return carbonization;
+	}
+
+	public int getCombustability() {
+		return combustability;
+	}
 }

src/main/java/forestry/api/arboriculture/EnumTreeChromosome.java

@@ -7,8 +7,6 @@ package forestry.api.arboriculture;
 
 import java.util.Locale;
 
-import net.minecraftforge.common.EnumPlantType;
-
 import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IAlleleArea;
 import forestry.api.genetics.IAlleleBoolean;
@@ -18,6 +16,7 @@ import forestry.api.genetics.IAllelePlantType;
 import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IFruitFamily;
 import forestry.api.genetics.ISpeciesRoot;
+import net.minecraftforge.common.EnumPlantType;
 
 public enum EnumTreeChromosome implements IChromosomeType {
 
@@ -28,7 +27,9 @@ public enum EnumTreeChromosome implements IChromosomeType {
 	SPECIES(IAlleleTreeSpecies.class),
 	/**
 	 * {@link IGrowthProvider}, determines conditions required by the tree to grow.
+	 * @deprecated unused
 	 */
+	@Deprecated
 	GROWTH(IAlleleGrowth.class),
 	/**
 	 * A float modifying the height of the tree. Taken into account at worldgen.
@@ -48,15 +49,19 @@ public enum EnumTreeChromosome implements IChromosomeType {
 	YIELD(IAlleleFloat.class),
 	/**
 	 * May add additional tolerances for {@link EnumPlantType}.
+	 * @deprecated this is tied to species directly
 	 */
+	@Deprecated
 	PLANT(IAllelePlantType.class),
 	/**
 	 * Determines the speed at which fruit will ripen on this tree.
 	 */
 	SAPPINESS(IAlleleFloat.class),
 	/**
-	 * Territory for leaf effects. Unused.
+	 * Territory for leaf effects.
+	 * @deprecated unused
 	 */
+	@Deprecated
 	TERRITORY(IAlleleArea.class),
 	/**
 	 * Leaf effect. Unused.
@@ -70,11 +75,15 @@ public enum EnumTreeChromosome implements IChromosomeType {
 	GIRTH(IAlleleInteger.class),
 	/**
 	 * The combustibility of the wood, when it burn to charcoal and the combustibility of the charcoal.
+	 * @deprecated this is tied to species directly
 	 */
+	@Deprecated
 	COMBUSTIBILITY(IAlleleInteger.class),
 	/**
 	 * The amount of charcoal that a wood pile ash drop;
+	 * @deprecated this is tied to species directly
 	 */
+	@Deprecated
 	CARBONIZATION(IAlleleInteger.class),
 	/**
 	 * Determines if the tree can burn.

src/main/java/forestry/api/arboriculture/EnumVanillaWoodType.java

@@ -7,12 +7,12 @@ import java.util.Random;
 import net.minecraft.block.BlockPlanks;
 
 public enum EnumVanillaWoodType implements IWoodType {
-	OAK(BlockPlanks.EnumType.OAK),
-	SPRUCE(BlockPlanks.EnumType.SPRUCE),
-	BIRCH(BlockPlanks.EnumType.BIRCH),
-	JUNGLE(BlockPlanks.EnumType.JUNGLE),
-	ACACIA(BlockPlanks.EnumType.ACACIA),
-	DARK_OAK(BlockPlanks.EnumType.DARK_OAK);
+	OAK(BlockPlanks.EnumType.OAK, 5, 20),
+	SPRUCE(BlockPlanks.EnumType.SPRUCE, 4, 19),
+	BIRCH(BlockPlanks.EnumType.BIRCH, 4, 19),
+	JUNGLE(BlockPlanks.EnumType.JUNGLE, 5, 20),
+	ACACIA(BlockPlanks.EnumType.ACACIA, 4, 20),
+	DARK_OAK(BlockPlanks.EnumType.DARK_OAK, 5, 20);
 
 	public static final EnumVanillaWoodType[] VALUES = values();
 
@@ -21,9 +21,13 @@ public enum EnumVanillaWoodType implements IWoodType {
 	}
 
 	private final BlockPlanks.EnumType vanillaType;
+	private final int carbonization;
+	private final int combustability;
 
-	EnumVanillaWoodType(BlockPlanks.EnumType vanillaType) {
+	EnumVanillaWoodType(BlockPlanks.EnumType vanillaType, int carbonization, int combustability) {
 		this.vanillaType = vanillaType;
+		this.carbonization = carbonization;
+		this.combustability = combustability;
 	}
 
 	public BlockPlanks.EnumType getVanillaType() {
@@ -57,4 +61,14 @@ public enum EnumVanillaWoodType implements IWoodType {
 	public float getHardness() {
 		return 2.0F;
 	}
+
+	@Override
+	public int getCarbonization() {
+		return carbonization;
+	}
+
+	@Override
+	public int getCombustability() {
+		return combustability;
+	}
 }

src/main/java/forestry/api/arboriculture/IGrowthProvider.java

@@ -10,6 +10,10 @@ import javax.annotation.Nullable;
 import net.minecraft.util.math.BlockPos;
 import net.minecraft.world.World;
 
+/**
+ * @deprecated this is being removed to simplify trees
+ */
+@Deprecated
 public interface IGrowthProvider {
 
 	/**
@@ -25,8 +29,6 @@ public interface IGrowthProvider {
 	@Nullable
 	BlockPos canGrow(ITreeGenome genome, World world, BlockPos pos, int expectedGirth, int expectedHeight);
 
-	EnumGrowthConditions getGrowthConditions(ITreeGenome genome, World world, BlockPos pos);
-
 	/**
 	 * @return Short, human-readable identifier used in the treealyzer.
 	 */

src/main/java/forestry/api/arboriculture/ITree.java

@@ -7,24 +7,19 @@ package forestry.api.arboriculture;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
-import java.util.EnumSet;
 import java.util.List;
 import java.util.Map;
 
+import com.mojang.authlib.GameProfile;
+import forestry.api.genetics.IEffectData;
+import forestry.api.genetics.IIndividual;
+import forestry.api.world.ITreeGenData;
 import net.minecraft.item.ItemStack;
 import net.minecraft.util.math.BlockPos;
 import net.minecraft.world.IBlockAccess;
 import net.minecraft.world.World;
 import net.minecraft.world.gen.feature.WorldGenerator;
 
-import com.mojang.authlib.GameProfile;
-
-import net.minecraftforge.common.EnumPlantType;
-
-import forestry.api.genetics.IEffectData;
-import forestry.api.genetics.IIndividual;
-import forestry.api.world.ITreeGenData;
-
 public interface ITree extends IIndividual, ITreeGenData {
 
 	void mate(ITree other);
@@ -39,8 +34,6 @@ public interface ITree extends IIndividual, ITreeGenData {
 
 	ITreeGenome getMate();
 
-	EnumSet<EnumPlantType> getPlantTypes();
-
 	/**
 	 * @since Forestry 4.0
 	 */
@@ -86,11 +79,6 @@ public interface ITree extends IIndividual, ITreeGenData {
 	@Override
 	int getGirth();
 
-	/**
-	 * @return Growth conditions at the given position.
-	 */
-	EnumGrowthConditions getGrowthCondition(World world, BlockPos pos);
-
 	WorldGenerator getTreeGenerator(World world, BlockPos pos, boolean wasBonemealed);
 
 	@Override

src/main/java/forestry/api/arboriculture/ITreeGenome.java

@@ -6,9 +6,6 @@
 package forestry.api.arboriculture;
 
 import javax.annotation.Nonnull;
-import java.util.EnumSet;
-
-import net.minecraftforge.common.EnumPlantType;
 
 import forestry.api.genetics.IGenome;
 
@@ -23,8 +20,6 @@ public interface ITreeGenome extends IGenome {
 	@Nonnull
 	IFruitProvider getFruitProvider();
 
-	IGrowthProvider getGrowthProvider();
-
 	float getHeight();
 
 	float getFertility();
@@ -37,18 +32,12 @@ public interface ITreeGenome extends IGenome {
 
 	float getSappiness();
 
-	EnumSet<EnumPlantType> getPlantTypes();
-
 	/**
 	 * @return Amount of random block ticks required for a sapling to mature into a fully grown tree.
 	 */
 	int getMaturationTime();
 
 	int getGirth();
-	
-	int getCombustibility();
-	
-	int getCarbonization();
 
 	IAlleleLeafEffect getEffect();
 }

src/main/java/forestry/api/arboriculture/ITreeRoot.java

@@ -8,18 +8,17 @@ package forestry.api.arboriculture;
 import javax.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
+import com.mojang.authlib.GameProfile;
+import forestry.api.genetics.IAllele;
+import forestry.api.genetics.IChromosome;
+import forestry.api.genetics.ISpeciesRoot;
 import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.util.math.BlockPos;
 import net.minecraft.world.World;
 
-import com.mojang.authlib.GameProfile;
-
-import forestry.api.genetics.IAllele;
-import forestry.api.genetics.IChromosome;
-import forestry.api.genetics.ISpeciesRoot;
-
 public interface ITreeRoot extends ISpeciesRoot {
 
 	@Override
@@ -82,7 +81,7 @@ public interface ITreeRoot extends ISpeciesRoot {
 	boolean setFruitBlock(World world, IAlleleFruit allele, float sappiness, BlockPos pos);
 
 	/* GAME MODE */
-	ArrayList<ITreekeepingMode> getTreekeepingModes();
+	List<ITreekeepingMode> getTreekeepingModes();
 
 	ITreekeepingMode getTreekeepingMode(World world);
 
@@ -98,6 +97,5 @@ public interface ITreeRoot extends ISpeciesRoot {
 
 	/* MUTATIONS */
 	@Override
-	Collection<ITreeMutation> getMutations(boolean shuffle);
-
+	List<ITreeMutation> getMutations(boolean shuffle);
 }

src/main/java/forestry/api/arboriculture/IWoodProvider.java

@@ -7,12 +7,12 @@ package forestry.api.arboriculture;
 
 import javax.annotation.Nonnull;
 
+import forestry.api.core.ITextureManager;
 import net.minecraft.client.renderer.texture.TextureAtlasSprite;
 import net.minecraft.item.Item;
 import net.minecraft.item.ItemStack;
 import net.minecraftforge.fml.relauncher.Side;
 import net.minecraftforge.fml.relauncher.SideOnly;
-import forestry.api.core.ITextureManager;
 
 public interface IWoodProvider {
 	@SideOnly(Side.CLIENT)
@@ -30,4 +30,14 @@ public interface IWoodProvider {
 	 * @return A stack of wood from the tree to craft wood pile's or other things.
 	 */
 	ItemStack getWoodStack();
+
+	/**
+	 * @return how long this wood's charcoal burns / 1000
+	 */
+	int getCombustibility();
+
+	/**
+	 * The amount of charcoal dropped from a charcoal pile of this wood.
+	 */
+	int getCarbonization();
 }

src/main/java/forestry/api/arboriculture/IWoodType.java

@@ -10,4 +10,8 @@ public interface IWoodType extends IStringSerializable {
 	int getMetadata();
 
 	float getHardness();
+
+	int getCarbonization();
+
+	int getCombustability();
 }

src/main/java/forestry/api/genetics/ICheckPollinatable.java

@@ -10,11 +10,8 @@
  ******************************************************************************/
 package forestry.api.genetics;
 
-import java.util.EnumSet;
-
-import net.minecraftforge.common.EnumPlantType;
-
 import forestry.api.arboriculture.ITree;
+import net.minecraftforge.common.EnumPlantType;
 
 /**
  * Used to check for pollination traits without altering the world by changing vanilla leaves to forestry ones.
@@ -23,10 +20,10 @@ import forestry.api.arboriculture.ITree;
 public interface ICheckPollinatable {
 
 	/**
-	 * @return plant types this pollinatable is classified as.
+	 * @return plant type this pollinatable is classified as.
 	 * (Can be used by bees to determine whether to interact or not.)
 	 */
-	EnumSet<EnumPlantType> getPlantType();
+	EnumPlantType getPlantType();
 
 	/**
 	 * @return IIndividual containing the genetic information of this IPollinatable

src/main/java/forestry/api/genetics/IMutationBuilder.java

@@ -5,13 +5,10 @@
  ******************************************************************************/
 package forestry.api.genetics;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.state.IBlockState;
-
-import net.minecraftforge.common.BiomeDictionary;
-
 import forestry.api.core.EnumHumidity;
 import forestry.api.core.EnumTemperature;
+import net.minecraft.block.state.IBlockState;
+import net.minecraftforge.common.BiomeDictionary;
 
 /** Set custom mutation requirements */
 public interface IMutationBuilder {
@@ -46,7 +43,7 @@ public interface IMutationBuilder {
 	IMutationBuilder requireNight();
 
 	/** Require a specific resource to be under the location of the mutation */
-	IMutationBuilder requireResource(IBlockState requiredBlockState);
+	IMutationBuilder requireResource(IBlockState... acceptedBlockStates);
 
 	IMutationBuilder requireResource(String oreDictName);
 

src/main/java/forestry/api/genetics/ISpeciesRoot.java

@@ -12,12 +12,11 @@ import java.util.List;
 import java.util.Map;
 import java.util.Random;
 
+import com.mojang.authlib.GameProfile;
 import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.world.World;
 
-import com.mojang.authlib.GameProfile;
-
 /**
  * Describes a class of species (i.e. bees, trees, butterflies), provides helper functions and access to common functionality.
  */
@@ -105,9 +104,9 @@ public interface ISpeciesRoot {
 	void registerTemplate(String identifier, IAllele[] template);
 
 	/**
-	 * Retrieves a registered template using the passed identifier.
+	 * Retrieves a registered template using the passed species unique identifier.
 	 *
-	 * @param identifier
+	 * @param identifier species UID
 	 * @return Array of {@link IAllele} representing a genome.
 	 */
 	IAllele[] getTemplate(String identifier);
@@ -139,13 +138,13 @@ public interface ISpeciesRoot {
 	/**
 	 * @return All registered mutations.
 	 */
-	Collection<? extends IMutation> getMutations(boolean shuffle);
+	List<? extends IMutation> getMutations(boolean shuffle);
 
 	/**
 	 * @param other Allele to match mutations against.
 	 * @return All registered mutations the given allele is part of.
 	 */
-	Collection<? extends IMutation> getCombinations(IAllele other);
+	List<? extends IMutation> getCombinations(IAllele other);
 
 	/**
 	 * @since Forestry 3.7
@@ -170,14 +169,14 @@ public interface ISpeciesRoot {
 	void setResearchSuitability(ItemStack itemstack, float suitability);
 
 	/**
-	 * @return Array of {@link IChromosomeType} which are in this species genome
+	 * @return Array of all {@link IChromosomeType} which are in this species genome
 	 */
 	IChromosomeType[] getKaryotype();
 
 	/**
-	 * @return {@link IChromosomeType} which is the "key" for this species class, usually the species chromosome.
+	 * @return {@link IChromosomeType} which is the "key" for this species class, the species chromosome.
 	 */
-	IChromosomeType getKaryotypeKey();
+	IChromosomeType getSpeciesChromosomeType();
 
 	/**
 	 * Plugin to add information for the handheld genetic analyzer.

src/main/java/forestry/api/lepidopterology/IButterflyRoot.java

@@ -7,18 +7,16 @@ package forestry.api.lepidopterology;
 
 import javax.annotation.Nullable;
 import java.util.ArrayList;
-import java.util.Collection;
+import java.util.List;
 
+import com.mojang.authlib.GameProfile;
+import forestry.api.genetics.IAllele;
+import forestry.api.genetics.ISpeciesRoot;
 import net.minecraft.entity.EntityLiving;
 import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.world.World;
 
-import com.mojang.authlib.GameProfile;
-
-import forestry.api.genetics.IAllele;
-import forestry.api.genetics.ISpeciesRoot;
-
 public interface IButterflyRoot extends ISpeciesRoot {
 
 	@Override
@@ -67,7 +65,7 @@ public interface IButterflyRoot extends ISpeciesRoot {
 
 	/* MUTATIONS */
 	@Override
-	Collection<IButterflyMutation> getMutations(boolean shuffle);
+	List<IButterflyMutation> getMutations(boolean shuffle);
 
 	@Nullable
 	@Override

src/main/java/forestry/api/multiblock/ICharcoalPileComponent.java

@@ -8,9 +8,8 @@ package forestry.api.multiblock;
 import javax.annotation.Nonnull;
 
 import com.mojang.authlib.GameProfile;
-
 import forestry.api.arboriculture.EnumPileType;
-import forestry.api.arboriculture.ITree;
+import forestry.api.arboriculture.IAlleleTreeSpecies;
 import net.minecraftforge.fml.relauncher.Side;
 import net.minecraftforge.fml.relauncher.SideOnly;
 
@@ -23,11 +22,10 @@ public interface ICharcoalPileComponent<T extends IMultiblockLogicCharcoalPile>
 	
 	@Override
 	T getMultiblockLogic();
-	
-	@Nonnull
-	ITree getTree();
-	
-	void setTree(@Nonnull ITree tree);
+
+	IAlleleTreeSpecies getTreeSpecies();
+
+	void setTreeSpecies(@Nonnull IAlleleTreeSpecies treeSpecies);
 	
 	@Override
 	@Nonnull
@@ -38,6 +36,6 @@ public interface ICharcoalPileComponent<T extends IMultiblockLogicCharcoalPile>
 	EnumPileType getPileType();
 	
 	@SideOnly(Side.CLIENT)
-	ITree getNextWoodPile();
+	IAlleleTreeSpecies getNextWoodPile();
 
 }

src/main/java/forestry/apiculture/BeekeepingLogic.java

@@ -239,9 +239,11 @@ public class BeekeepingLogic implements IBeekeepingLogic, IStreamable {
 
 	@Override
 	public void clearCachedValues() {
-		hasFlowersCache.clear();
-		queenCanWorkCache.clear();
-		canWork();
+		if (!housing.getWorldObj().isRemote) {
+			hasFlowersCache.clear();
+			queenCanWorkCache.clear();
+			canWork();
+		}
 	}
 
 	private void queenWorkTick(IBee queen) {

src/main/java/forestry/apiculture/compat/ApicultureJeiPlugin.java

@@ -5,16 +5,15 @@ import javax.annotation.Nullable;
 import java.util.Arrays;
 import java.util.List;
 
-import net.minecraft.item.ItemStack;
-
+import forestry.api.apiculture.BeeManager;
 import forestry.api.genetics.IAlleleSpecies;
 import forestry.apiculture.PluginApiculture;
-import forestry.apiculture.genetics.BeeGenome;
-
+import forestry.core.genetics.Genome;
 import mezz.jei.api.BlankModPlugin;
 import mezz.jei.api.IModRegistry;
 import mezz.jei.api.ISubtypeRegistry;
 import mezz.jei.api.JEIPlugin;
+import net.minecraft.item.ItemStack;
 
 @JEIPlugin
 public class ApicultureJeiPlugin extends BlankModPlugin {
@@ -51,7 +50,7 @@ public class ApicultureJeiPlugin extends BlankModPlugin {
 		@Nullable
 		@Override
 		public String getSubtypeInfo(@Nonnull ItemStack itemStack) {
-			IAlleleSpecies species = BeeGenome.getSpeciesDirectly(itemStack);
+			IAlleleSpecies species = Genome.getSpeciesDirectly(BeeManager.beeRoot, itemStack);
 			return species == null ? null : species.getUID();
 		}
 	}

src/main/java/forestry/apiculture/entities/AIAvoidPlayers.java

@@ -66,7 +66,7 @@ public class AIAvoidPlayers extends EntityAIBase {
 		}
 
 		path = pathNavigator.getPathToXYZ(randomTarget.xCoord, randomTarget.yCoord, randomTarget.zCoord);
-		return path != null && path.isDestinationSame(randomTarget);
+		return path != null;
 	}
 
 	@Override

src/main/java/forestry/apiculture/flowers/FlowerProvider.java

@@ -10,19 +10,15 @@
  ******************************************************************************/
 package forestry.apiculture.flowers;
 
-import java.util.EnumSet;
-
-import net.minecraft.item.ItemStack;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
-import net.minecraftforge.common.EnumPlantType;
-
 import forestry.api.apiculture.FlowerManager;
 import forestry.api.genetics.ICheckPollinatable;
 import forestry.api.genetics.IFlowerProvider;
 import forestry.api.genetics.IIndividual;
 import forestry.core.utils.Translator;
+import net.minecraft.item.ItemStack;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
+import net.minecraftforge.common.EnumPlantType;
 
 public class FlowerProvider implements IFlowerProvider {
 
@@ -42,15 +38,15 @@ public class FlowerProvider implements IFlowerProvider {
 	@Override
 	public boolean isAcceptedPollinatable(World world, ICheckPollinatable pollinatable) {
 
-		EnumSet<EnumPlantType> plantTypes = pollinatable.getPlantType();
+		EnumPlantType plantType = pollinatable.getPlantType();
 
 		switch (flowerType) {
 			case FlowerManager.FlowerTypeNether:
-				return plantTypes.contains(EnumPlantType.Nether);
+				return plantType == EnumPlantType.Nether;
 			case FlowerManager.FlowerTypeCacti:
-				return plantTypes.contains(EnumPlantType.Desert);
+				return plantType == EnumPlantType.Desert;
 			default:
-				return plantTypes.size() > 1 || !plantTypes.contains(EnumPlantType.Nether);
+				return plantType != EnumPlantType.Nether;
 		}
 	}
 

src/main/java/forestry/apiculture/genetics/BeeGenome.java

@@ -10,17 +10,12 @@
  ******************************************************************************/
 package forestry.apiculture.genetics;
 
-import com.google.common.cache.CacheBuilder;
-import com.google.common.cache.CacheLoader;
-import com.google.common.cache.LoadingCache;
-
 import javax.annotation.Nonnull;
 import java.util.concurrent.TimeUnit;
 
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.util.math.Vec3i;
-
+import com.google.common.cache.CacheBuilder;
+import com.google.common.cache.CacheLoader;
+import com.google.common.cache.LoadingCache;
 import forestry.api.apiculture.BeeManager;
 import forestry.api.apiculture.EnumBeeChromosome;
 import forestry.api.apiculture.IAlleleBeeEffect;
@@ -38,6 +33,9 @@ import forestry.core.genetics.Genome;
 import forestry.core.genetics.alleles.AlleleArea;
 import forestry.core.genetics.alleles.AlleleBoolean;
 import forestry.core.genetics.alleles.AlleleTolerance;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.util.math.Vec3i;
 
 public class BeeGenome extends Genome implements IBeeGenome {
 	/**
@@ -90,7 +88,7 @@ public class BeeGenome extends Genome implements IBeeGenome {
 			return null;
 		}
 
-		IAlleleSpecies species = getSpeciesDirectly(itemStack);
+		IAlleleSpecies species = getSpeciesDirectly(BeeManager.beeRoot, itemStack);
 		if (species instanceof IAlleleBeeSpecies) {
 			return (IAlleleBeeSpecies) species;
 		}

src/main/java/forestry/apiculture/genetics/BeeRoot.java

@@ -12,20 +12,12 @@ package forestry.apiculture.genetics;
 
 import javax.annotation.Nullable;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Collections;
+import java.util.List;
 import java.util.Locale;
 import java.util.Map.Entry;
 
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.world.World;
-
 import com.mojang.authlib.GameProfile;
-
-import net.minecraftforge.fml.common.FMLCommonHandler;
-
 import forestry.api.apiculture.BeeManager;
 import forestry.api.apiculture.EnumBeeChromosome;
 import forestry.api.apiculture.EnumBeeType;
@@ -53,6 +45,11 @@ import forestry.apiculture.BeeHousingModifier;
 import forestry.apiculture.BeekeepingLogic;
 import forestry.apiculture.PluginApiculture;
 import forestry.core.genetics.SpeciesRoot;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.world.World;
+import net.minecraftforge.fml.common.FMLCommonHandler;
 
 public class BeeRoot extends SpeciesRoot implements IBeeRoot {
 
@@ -252,10 +249,10 @@ public class BeeRoot extends SpeciesRoot implements IBeeRoot {
 	/**
 	 * List of possible mutations on species alleles.
 	 */
-	private static final ArrayList<IBeeMutation> beeMutations = new ArrayList<>();
+	private static final List<IBeeMutation> beeMutations = new ArrayList<>();
 
 	@Override
-	public Collection<IBeeMutation> getMutations(boolean shuffle) {
+	public List<IBeeMutation> getMutations(boolean shuffle) {
 		if (shuffle) {
 			Collections.shuffle(beeMutations);
 		}
@@ -371,7 +368,7 @@ public class BeeRoot extends SpeciesRoot implements IBeeRoot {
 	}
 
 	@Override
-	public IChromosomeType getKaryotypeKey() {
+	public IChromosomeType getSpeciesChromosomeType() {
 		return EnumBeeChromosome.SPECIES;
 	}
 

src/main/java/forestry/apiculture/genetics/JubilanceFactory.java

@@ -10,10 +10,9 @@
  ******************************************************************************/
 package forestry.apiculture.genetics;
 
-import net.minecraft.block.Block;
-
 import forestry.api.apiculture.IJubilanceFactory;
 import forestry.api.apiculture.IJubilanceProvider;
+import net.minecraft.block.state.IBlockState;
 
 public class JubilanceFactory implements IJubilanceFactory {
 	@Override
@@ -22,7 +21,7 @@ public class JubilanceFactory implements IJubilanceFactory {
 	}
 
 	@Override
-	public IJubilanceProvider getRequiresResource(Block block, int meta) {
-		return new JubilanceRequiresResource(block, meta);
+	public IJubilanceProvider getRequiresResource(IBlockState... acceptedBlockStates) {
+		return new JubilanceRequiresResource(acceptedBlockStates);
 	}
 }

src/main/java/forestry/apiculture/genetics/JubilanceRequiresResource.java

@@ -10,33 +10,40 @@
  ******************************************************************************/
 package forestry.apiculture.genetics;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.item.ItemStack;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
 
 import forestry.api.apiculture.IAlleleBeeSpecies;
 import forestry.api.apiculture.IBeeGenome;
 import forestry.api.apiculture.IBeeHousing;
 import forestry.api.apiculture.IJubilanceProvider;
-import forestry.core.utils.ItemStackUtil;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.tileentity.TileEntity;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
 
 public class JubilanceRequiresResource implements IJubilanceProvider {
 
-	private final ItemStack blockRequired;
+	private final Set<IBlockState> acceptedBlockStates = new HashSet<>();
 
-	public JubilanceRequiresResource(Block block, int meta) {
-		this.blockRequired = new ItemStack(block, meta);
+	public JubilanceRequiresResource(IBlockState... acceptedBlockStates) {
+		Collections.addAll(this.acceptedBlockStates, acceptedBlockStates);
 	}
 
 	@Override
 	public boolean isJubilant(IAlleleBeeSpecies species, IBeeGenome genome, IBeeHousing housing) {
 		World world = housing.getWorldObj();
-		BlockPos housingCoords = housing.getCoordinates();
+		BlockPos pos = housing.getCoordinates();
 
-		IBlockState state = world.getBlockState(housingCoords.down());
-		return ItemStackUtil.equals(state, blockRequired);
+		TileEntity tile;
+		do {
+			pos = pos.down();
+			tile = world.getTileEntity(pos);
+		} while (tile instanceof IBeeHousing && pos.getY() > 0);
+
+		IBlockState blockState = world.getBlockState(pos);
+		return this.acceptedBlockStates.contains(blockState);
 	}
 
 }

src/main/java/forestry/apiculture/items/ItemHiveFrame.java

@@ -57,7 +57,7 @@ public class ItemHiveFrame extends ItemForestry implements IHiveFrame {
 		super.addInformation(stack, playerIn, tooltip, advanced);
 		beeModifier.addInformation(stack, playerIn, tooltip, advanced);
 		if (!stack.isItemDamaged()) {
-			tooltip.add(Translator.translateToLocalFormatted("item.for.frame.durability", stack.getMaxDamage()));
+			tooltip.add(Translator.translateToLocalFormatted("item.for.durability", stack.getMaxDamage()));
 		}
 	}
 

src/main/java/forestry/apiculture/worldgen/VillageApiaristHouse.java

@@ -69,7 +69,6 @@ public class VillageApiaristHouse extends StructureVillagePieces.House1 {
 	private static final Random random = new Random();
 
 	private int averageGroundLevel = -1;
-	private boolean isInDesert = false;
 	private IBlockState planks;
 	private IBlockState slabs;
 	private IBlockState logs;
@@ -86,8 +85,6 @@ public class VillageApiaristHouse extends StructureVillagePieces.House1 {
 	public VillageApiaristHouse(StructureVillagePieces.Start startPiece, int componentType, Random random, StructureBoundingBox boundingBox, EnumFacing facing) {
 		super(startPiece, componentType, random, boundingBox, facing);
 
-		isInDesert = startPiece.inDesert;
-
 		createBuildingBlocks(random);
 	}
 
@@ -280,7 +277,7 @@ public class VillageApiaristHouse extends StructureVillagePieces.House1 {
 	private void buildGarden(World world, StructureBoundingBox box) {
 
 		Block ground = Blocks.DIRT;
-		if (isInDesert) {
+		if (field_189928_h == 1) { // desert
 			ground = Blocks.SAND;
 		}
 
@@ -293,7 +290,7 @@ public class VillageApiaristHouse extends StructureVillagePieces.House1 {
 
 	private void plantFlowerGarden(World world, StructureBoundingBox box, int minX, int minY, int minZ, int maxX, int maxY, int maxZ) {
 
-		if (isInDesert) {
+		if (field_189928_h == 1) { // desert
 			setBlockState(world, Blocks.CACTUS.getDefaultState(), 4, 1, 7, box);
 			return;
 		}

src/main/java/forestry/arboriculture/PluginArboriculture.java

@@ -17,34 +17,12 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.BlockLeaves;
-import net.minecraft.block.BlockNewLeaf;
-import net.minecraft.block.BlockOldLeaf;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.entity.passive.EntityVillager;
-import net.minecraft.init.Blocks;
-import net.minecraft.init.Items;
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-
-import net.minecraftforge.client.event.TextureStitchEvent;
-import net.minecraftforge.common.MinecraftForge;
-import net.minecraftforge.fml.common.IFuelHandler;
-import net.minecraftforge.fml.common.SidedProxy;
-import net.minecraftforge.fml.common.event.FMLInterModComms.IMCMessage;
-import net.minecraftforge.fml.common.eventhandler.SubscribeEvent;
-import net.minecraftforge.fml.common.registry.GameRegistry;
-import net.minecraftforge.fml.common.registry.VillagerRegistry;
-import net.minecraftforge.fml.relauncher.Side;
-import net.minecraftforge.fml.relauncher.SideOnly;
-import net.minecraftforge.oredict.OreDictionary;
-
 import forestry.api.arboriculture.EnumForestryWoodType;
 import forestry.api.arboriculture.EnumGermlingType;
 import forestry.api.arboriculture.EnumPileType;
 import forestry.api.arboriculture.EnumVanillaWoodType;
 import forestry.api.arboriculture.IAlleleFruit;
+import forestry.api.arboriculture.IAlleleTreeSpecies;
 import forestry.api.arboriculture.ITree;
 import forestry.api.arboriculture.IWoodType;
 import forestry.api.arboriculture.TreeManager;
@@ -56,6 +34,7 @@ import forestry.api.genetics.ISaplingTranslator;
 import forestry.api.recipes.RecipeManagers;
 import forestry.api.storage.ICrateRegistry;
 import forestry.api.storage.StorageManager;
+import forestry.arboriculture.blocks.BlockForestryLeaves;
 import forestry.arboriculture.blocks.BlockPile;
 import forestry.arboriculture.blocks.BlockRegistryArboriculture;
 import forestry.arboriculture.blocks.log.BlockArbLog;
@@ -71,6 +50,7 @@ import forestry.arboriculture.genetics.alleles.AlleleFruit;
 import forestry.arboriculture.genetics.alleles.AlleleGrowth;
 import forestry.arboriculture.genetics.alleles.AlleleLeafEffect;
 import forestry.arboriculture.items.ItemCharcoal;
+import forestry.arboriculture.items.ItemGrafter;
 import forestry.arboriculture.items.ItemRegistryArboriculture;
 import forestry.arboriculture.models.TextureLeaves;
 import forestry.arboriculture.network.PacketRegistryArboriculture;
@@ -95,6 +75,31 @@ import forestry.factory.recipes.FabricatorRecipe;
 import forestry.plugins.BlankForestryPlugin;
 import forestry.plugins.ForestryPlugin;
 import forestry.plugins.ForestryPluginUids;
+import net.minecraft.block.Block;
+import net.minecraft.block.BlockLeaves;
+import net.minecraft.block.BlockNewLeaf;
+import net.minecraft.block.BlockOldLeaf;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.entity.passive.EntityVillager;
+import net.minecraft.entity.player.EntityPlayer;
+import net.minecraft.init.Blocks;
+import net.minecraft.init.Items;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.util.EnumHand;
+import net.minecraft.world.World;
+import net.minecraftforge.client.event.TextureStitchEvent;
+import net.minecraftforge.common.MinecraftForge;
+import net.minecraftforge.event.world.BlockEvent;
+import net.minecraftforge.fml.common.IFuelHandler;
+import net.minecraftforge.fml.common.SidedProxy;
+import net.minecraftforge.fml.common.event.FMLInterModComms.IMCMessage;
+import net.minecraftforge.fml.common.eventhandler.SubscribeEvent;
+import net.minecraftforge.fml.common.registry.GameRegistry;
+import net.minecraftforge.fml.common.registry.VillagerRegistry;
+import net.minecraftforge.fml.relauncher.Side;
+import net.minecraftforge.fml.relauncher.SideOnly;
+import net.minecraftforge.oredict.OreDictionary;
 
 @ForestryPlugin(pluginID = ForestryPluginUids.ARBORICULTURE, name = "Arboriculture", author = "Binnie & SirSengir", url = Constants.URL, unlocalizedDescription = "for.plugin.arboriculture.description")
 public class PluginArboriculture extends BlankForestryPlugin {
@@ -395,10 +400,11 @@ public class PluginArboriculture extends BlankForestryPlugin {
 				'Y', "chestWood");
 		
 		//Wood Piles
-		for(ITree tree : TreeManager.treeRoot.getIndividualTemplates()){
-			ItemStack log = tree.getGenome().getPrimary().getWoodProvider().getWoodStack().copy();
+		for (ITree tree : TreeManager.treeRoot.getIndividualTemplates()) {
+			IAlleleTreeSpecies treeSpecies = tree.getGenome().getPrimary();
+			ItemStack log = treeSpecies.getWoodProvider().getWoodStack().copy();
 			log.stackSize = 1;
-			ItemStack woodPile = BlockPile.createWoodPile(tree);
+			ItemStack woodPile = BlockPile.createWoodPile(treeSpecies);
 			RecipeUtil.addShapelessRecipe(woodPile, log, log, log, log);
 		}
 		
@@ -546,4 +552,31 @@ public class PluginArboriculture extends BlankForestryPlugin {
 			alleleFruit.getProvider().registerSprites();
 		}
 	}
+
+	@SubscribeEvent
+	public void onHarvestDropsEvent(BlockEvent.HarvestDropsEvent event) {
+		IBlockState state = event.getState();
+		Block block = state.getBlock();
+		if (block instanceof BlockLeaves && !(block instanceof BlockForestryLeaves)) {
+			EntityPlayer player = event.getHarvester();
+			if (player != null) {
+				ItemStack harvestingTool = player.getHeldItemMainhand();
+				if (harvestingTool != null && harvestingTool.getItem() instanceof ItemGrafter) {
+					if (event.getDrops().isEmpty()) {
+						World world = event.getWorld();
+						Item itemDropped = block.getItemDropped(state, world.rand, 3);
+						if (itemDropped != null) {
+							event.getDrops().add(new ItemStack(itemDropped, 1, block.damageDropped(state)));
+						}
+					}
+
+					harvestingTool.damageItem(1, player);
+					if (harvestingTool.stackSize <= 0) {
+						net.minecraftforge.event.ForgeEventFactory.onPlayerDestroyItem(player, harvestingTool, EnumHand.MAIN_HAND);
+						player.setHeldItem(EnumHand.MAIN_HAND, null);
+					}
+				}
+			}
+		}
+	}
 }

src/main/java/forestry/arboriculture/VillagerArboristTrades.java

@@ -7,12 +7,6 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Random;
 
-import net.minecraft.entity.passive.EntityVillager;
-import net.minecraft.init.Items;
-import net.minecraft.item.ItemStack;
-import net.minecraft.village.MerchantRecipe;
-import net.minecraft.village.MerchantRecipeList;
-
 import forestry.api.arboriculture.EnumForestryWoodType;
 import forestry.api.arboriculture.EnumGermlingType;
 import forestry.api.arboriculture.TreeManager;
@@ -22,6 +16,11 @@ import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IIndividual;
+import net.minecraft.entity.passive.EntityVillager;
+import net.minecraft.init.Items;
+import net.minecraft.item.ItemStack;
+import net.minecraft.village.MerchantRecipe;
+import net.minecraft.village.MerchantRecipeList;
 
 public class VillagerArboristTrades {
 
@@ -120,7 +119,7 @@ public class VillagerArboristTrades {
 				j = this.emeraldPriceInfo.getPrice(random);
 			}
 
-			IChromosomeType treeSpeciesType = TreeManager.treeRoot.getKaryotypeKey();
+			IChromosomeType treeSpeciesType = TreeManager.treeRoot.getSpeciesChromosomeType();
 			Collection<IAllele> registeredSpecies = AlleleManager.alleleRegistry.getRegisteredAlleles(treeSpeciesType);
 			List<IAlleleSpecies> potentialSpecies = new ArrayList<>();
 			for (IAllele allele : registeredSpecies) {

src/main/java/forestry/arboriculture/blocks/BlockForestryLeaves.java

@@ -16,6 +16,29 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Random;
 
+import com.mojang.authlib.GameProfile;
+import forestry.api.arboriculture.EnumGermlingType;
+import forestry.api.arboriculture.IToolGrafter;
+import forestry.api.arboriculture.ITree;
+import forestry.api.arboriculture.TreeManager;
+import forestry.api.core.IItemModelRegister;
+import forestry.api.core.IModelManager;
+import forestry.api.core.IToolScoop;
+import forestry.api.core.Tabs;
+import forestry.api.lepidopterology.ButterflyManager;
+import forestry.api.lepidopterology.EnumFlutterType;
+import forestry.api.lepidopterology.IButterfly;
+import forestry.arboriculture.LeafDecayHelper;
+import forestry.arboriculture.PluginArboriculture;
+import forestry.arboriculture.genetics.TreeDefinition;
+import forestry.arboriculture.tiles.TileLeaves;
+import forestry.core.blocks.IColoredBlock;
+import forestry.core.blocks.propertys.UnlistedBlockAccess;
+import forestry.core.blocks.propertys.UnlistedBlockPos;
+import forestry.core.proxy.Proxies;
+import forestry.core.tiles.TileUtil;
+import forestry.core.utils.BlockUtil;
+import forestry.core.utils.ItemStackUtil;
 import net.minecraft.block.BlockLeaves;
 import net.minecraft.block.BlockPlanks;
 import net.minecraft.block.IGrowable;
@@ -40,9 +63,6 @@ import net.minecraft.util.math.BlockPos;
 import net.minecraft.util.math.RayTraceResult;
 import net.minecraft.world.IBlockAccess;
 import net.minecraft.world.World;
-
-import com.mojang.authlib.GameProfile;
-
 import net.minecraftforge.client.model.ModelLoader;
 import net.minecraftforge.common.property.ExtendedBlockState;
 import net.minecraftforge.common.property.IExtendedBlockState;
@@ -50,29 +70,6 @@ import net.minecraftforge.common.property.IUnlistedProperty;
 import net.minecraftforge.fml.relauncher.Side;
 import net.minecraftforge.fml.relauncher.SideOnly;
 
-import forestry.api.arboriculture.EnumGermlingType;
-import forestry.api.arboriculture.IToolGrafter;
-import forestry.api.arboriculture.ITree;
-import forestry.api.arboriculture.TreeManager;
-import forestry.api.core.IItemModelRegister;
-import forestry.api.core.IModelManager;
-import forestry.api.core.IToolScoop;
-import forestry.api.core.Tabs;
-import forestry.api.lepidopterology.ButterflyManager;
-import forestry.api.lepidopterology.EnumFlutterType;
-import forestry.api.lepidopterology.IButterfly;
-import forestry.arboriculture.LeafDecayHelper;
-import forestry.arboriculture.PluginArboriculture;
-import forestry.arboriculture.genetics.TreeDefinition;
-import forestry.arboriculture.tiles.TileLeaves;
-import forestry.core.blocks.IColoredBlock;
-import forestry.core.blocks.propertys.UnlistedBlockAccess;
-import forestry.core.blocks.propertys.UnlistedBlockPos;
-import forestry.core.proxy.Proxies;
-import forestry.core.tiles.TileUtil;
-import forestry.core.utils.BlockUtil;
-import forestry.core.utils.ItemStackUtil;
-
 public class BlockForestryLeaves extends BlockLeaves implements ITileEntityProvider, IGrowable, IItemModelRegister, IColoredBlock {
 
 	public BlockForestryLeaves() {
@@ -137,17 +134,16 @@ public class BlockForestryLeaves extends BlockLeaves implements ITileEntityProvi
 		int fortune = EnchantmentHelper.getEnchantmentLevel(Enchantments.FORTUNE, player.getActiveItemStack());
 		float saplingModifier = 1.0f;
 
-		if (!world.isRemote) {
-			ItemStack held = player.inventory.getCurrentItem();
-			if (held != null && held.getItem() instanceof IToolGrafter) {
-				saplingModifier = ((IToolGrafter) held.getItem()).getSaplingModifier(held, world, player, pos);
-				held.damageItem(1, player);
-				if (held.stackSize <= 0) {
-					net.minecraftforge.event.ForgeEventFactory.onPlayerDestroyItem(player, held, EnumHand.MAIN_HAND);
-					player.setHeldItem(EnumHand.MAIN_HAND, null);
-				}
+		ItemStack held = player.inventory.getCurrentItem();
+		if (held != null && held.getItem() instanceof IToolGrafter) {
+			saplingModifier = ((IToolGrafter) held.getItem()).getSaplingModifier(held, world, player, pos);
+			held.damageItem(1, player);
+			if (held.stackSize <= 0) {
+				net.minecraftforge.event.ForgeEventFactory.onPlayerDestroyItem(player, held, EnumHand.MAIN_HAND);
+				player.setHeldItem(EnumHand.MAIN_HAND, null);
 			}
 		}
+
 		GameProfile playerProfile = player.getGameProfile();
 		List<ItemStack> leafDrops = getLeafDrop(world, playerProfile, pos, saplingModifier, fortune);
 		drops.set(leafDrops);

src/main/java/forestry/arboriculture/blocks/BlockPile.java

@@ -1,7 +1,5 @@
 package forestry.arboriculture.blocks;
 
-import com.google.common.collect.Lists;
-
 import javax.annotation.Nonnull;
 import java.util.ArrayList;
 import java.util.EnumMap;
@@ -9,6 +7,36 @@ import java.util.List;
 import java.util.Map;
 import java.util.Random;
 
+import com.google.common.collect.Lists;
+import forestry.api.arboriculture.EnumPileType;
+import forestry.api.arboriculture.IAlleleTreeSpecies;
+import forestry.api.arboriculture.ITree;
+import forestry.api.arboriculture.IWoodProvider;
+import forestry.api.arboriculture.TreeManager;
+import forestry.api.core.IModelManager;
+import forestry.api.core.ISpriteRegister;
+import forestry.api.core.IStateMapperRegister;
+import forestry.api.core.ITextureManager;
+import forestry.api.core.Tabs;
+import forestry.api.genetics.AlleleManager;
+import forestry.api.genetics.IAllele;
+import forestry.api.multiblock.ICharcoalPileComponent;
+import forestry.apiculture.blocks.BlockCandle;
+import forestry.arboriculture.PluginArboriculture;
+import forestry.arboriculture.genetics.Tree;
+import forestry.arboriculture.multiblock.EnumPilePosition;
+import forestry.arboriculture.multiblock.ICharcoalPileControllerInternal;
+import forestry.arboriculture.render.PileParticleCallback;
+import forestry.arboriculture.render.PileStateMapper;
+import forestry.arboriculture.tiles.TilePile;
+import forestry.core.PluginCore;
+import forestry.core.blocks.BlockStructure;
+import forestry.core.blocks.propertys.UnlistedBlockAccess;
+import forestry.core.blocks.propertys.UnlistedBlockPos;
+import forestry.core.multiblock.MultiblockLogic;
+import forestry.core.proxy.Proxies;
+import forestry.core.render.ParticleHelper;
+import forestry.core.tiles.TileUtil;
 import net.minecraft.block.Block;
 import net.minecraft.block.ITileEntityProvider;
 import net.minecraft.block.SoundType;
@@ -40,42 +68,12 @@ import net.minecraft.util.text.TextComponentString;
 import net.minecraft.util.text.TextComponentTranslation;
 import net.minecraft.world.IBlockAccess;
 import net.minecraft.world.World;
-
 import net.minecraftforge.common.property.ExtendedBlockState;
 import net.minecraftforge.common.property.IExtendedBlockState;
 import net.minecraftforge.common.property.IUnlistedProperty;
 import net.minecraftforge.fml.relauncher.Side;
 import net.minecraftforge.fml.relauncher.SideOnly;
 
-import forestry.api.arboriculture.EnumPileType;
-import forestry.api.arboriculture.IAlleleTreeSpecies;
-import forestry.api.arboriculture.ITree;
-import forestry.api.arboriculture.TreeManager;
-import forestry.api.core.IModelManager;
-import forestry.api.core.ISpriteRegister;
-import forestry.api.core.IStateMapperRegister;
-import forestry.api.core.ITextureManager;
-import forestry.api.core.Tabs;
-import forestry.api.genetics.AlleleManager;
-import forestry.api.genetics.IAllele;
-import forestry.api.multiblock.ICharcoalPileComponent;
-import forestry.apiculture.blocks.BlockCandle;
-import forestry.arboriculture.PluginArboriculture;
-import forestry.arboriculture.genetics.Tree;
-import forestry.arboriculture.multiblock.EnumPilePosition;
-import forestry.arboriculture.multiblock.ICharcoalPileControllerInternal;
-import forestry.arboriculture.render.PileParticleCallback;
-import forestry.arboriculture.render.PileStateMapper;
-import forestry.arboriculture.tiles.TilePile;
-import forestry.core.PluginCore;
-import forestry.core.blocks.BlockStructure;
-import forestry.core.blocks.propertys.UnlistedBlockAccess;
-import forestry.core.blocks.propertys.UnlistedBlockPos;
-import forestry.core.multiblock.MultiblockLogic;
-import forestry.core.proxy.Proxies;
-import forestry.core.render.ParticleHelper;
-import forestry.core.tiles.TileUtil;
-
 public abstract class BlockPile extends BlockStructure implements ITileEntityProvider, IStateMapperRegister, ISpriteRegister {
 
     /**
@@ -318,13 +316,15 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 	@SideOnly(Side.CLIENT)
 	@Override
 	public void getSubBlocks(Item item, CreativeTabs tab, List<ItemStack> subItems) {
-		if(getPileType() == EnumPileType.WOOD){
+		if (getPileType() == EnumPileType.WOOD) {
 			List<ItemStack> woodPiles = new ArrayList<>();
-			for(ITree tree : TreeManager.treeRoot.getIndividualTemplates()) {
-				woodPiles.add(createWoodPile(tree));
+			for (ITree tree : TreeManager.treeRoot.getIndividualTemplates()) {
+				IAlleleTreeSpecies treeSpecies = tree.getGenome().getPrimary();
+				ItemStack woodPile = createWoodPile(treeSpecies);
+				woodPiles.add(woodPile);
 			}
 			subItems.addAll(woodPiles);
-		}else if(getPileType() == EnumPileType.DIRT){
+		} else if (getPileType() == EnumPileType.DIRT) {
 			super.getSubBlocks(item, tab, subItems);
 		}
 	}
@@ -412,8 +412,9 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 			ICharcoalPileComponent pile = (ICharcoalPileComponent) tile;
 
 			if (getPileType() == EnumPileType.ASH) {
-				if (pile.getTree() != null) {
-					ItemStack charcoal = new ItemStack(PluginArboriculture.items.charcoal, pile.getTree().getGenome().getCarbonization(), pile.getTree().getGenome().getCombustibility());
+				if (pile.getTreeSpecies() != null) {
+					IWoodProvider woodProvider = pile.getTreeSpecies().getWoodProvider();
+					ItemStack charcoal = new ItemStack(PluginArboriculture.items.charcoal, woodProvider.getCarbonization(), woodProvider.getCombustibility());
 					list.add(charcoal);
 					list.add(new ItemStack(PluginCore.items.ash, 3));
 				} else {
@@ -423,7 +424,7 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 			} else if (getPileType() == EnumPileType.DIRT) {
 				list.add(new ItemStack(this));
 			} else {
-				list.add(createWoodPile(pile.getTree()));
+				list.add(createWoodPile(pile.getTreeSpecies()));
 			}
 		}
 		return list;
@@ -485,7 +486,7 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 		if(getPileType() == EnumPileType.WOOD){
 			TileEntity tile = world.getTileEntity(pos);
 			if (tile instanceof ICharcoalPileComponent) {
-				return createWoodPile(((ICharcoalPileComponent) tile).getTree());
+				return createWoodPile(((ICharcoalPileComponent) tile).getTreeSpecies());
 			}
 		}else if(getPileType() == EnumPileType.DIRT){
 			return super.getPickBlock(state, target, world, pos, player);
@@ -528,10 +529,19 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 		IBlockState blockState = world.getBlockState(pos);
 		return ParticleHelper.addDestroyEffects(world, this, blockState, pos, effectRenderer, particleCallback);
 	}
-	
-	public static ITree getTree(ItemStack stack){
+
+	public static IAlleleTreeSpecies getTreeSpecies(ItemStack stack) {
 		if (stack != null) {
-			return new Tree(stack.getTagCompound().getCompoundTag("ContainedTree"));
+			NBTTagCompound tagCompound = stack.getTagCompound();
+
+			// legacy
+			if (tagCompound.hasKey("ContainedTree")) {
+				ITree tree = new Tree(tagCompound.getCompoundTag("ContainedTree"));
+				return tree.getGenome().getPrimary();
+			}
+
+			String treeSpeciesUid = tagCompound.getString("TreeSpecies");
+			return (IAlleleTreeSpecies) AlleleManager.alleleRegistry.getAllele(treeSpeciesUid);
 		}
 		return null;
 	}
@@ -541,10 +551,9 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 		if(getPileType() == EnumPileType.WOOD){
 			TileEntity tile = world.getTileEntity(pos);
 			if (tile instanceof ICharcoalPileComponent) {
-				
-				ITree tree = ((ICharcoalPileComponent)tile).getTree();
-				if(tree != null){
-					ItemStack wood = tree.getGenome().getPrimary().getWoodProvider().getWoodStack();
+				IAlleleTreeSpecies tree = ((ICharcoalPileComponent) tile).getTreeSpecies();
+				if (tree != null) {
+					ItemStack wood = tree.getWoodProvider().getWoodStack();
 					if(wood != null){
 						Block block = Block.getBlockFromItem(wood.getItem());
 						return block.getFlammability(world, pos, face);
@@ -560,10 +569,9 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 		if(getPileType() == EnumPileType.WOOD){
 			TileEntity tile = world.getTileEntity(pos);
 			if (tile instanceof ICharcoalPileComponent) {
-				
-				ITree tree = ((ICharcoalPileComponent)tile).getTree();
+				IAlleleTreeSpecies tree = ((ICharcoalPileComponent) tile).getTreeSpecies();
 				if(tree != null){
-					ItemStack wood = tree.getGenome().getPrimary().getWoodProvider().getWoodStack();
+					ItemStack wood = tree.getWoodProvider().getWoodStack();
 					if(wood != null){
 						Block block = Block.getBlockFromItem(wood.getItem());
 						return block.getFireSpreadSpeed(world, pos, face);
@@ -580,11 +588,11 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 		if(getPileType() == EnumPileType.WOOD){
 			TileEntity tile = world.getTileEntity(pos);
 			if (tile instanceof ICharcoalPileComponent) {
-				
-				ITree tree = ((ICharcoalPileComponent)tile).getTree();
+
+				IAlleleTreeSpecies tree = ((ICharcoalPileComponent) tile).getTreeSpecies();
 				if(tree != null){
-					ItemStack wood = tree.getGenome().getPrimary().getWoodProvider().getWoodStack();
-					if(wood != null){
+					ItemStack wood = tree.getWoodProvider().getWoodStack();
+					if (wood != null) {
 						Block block = Block.getBlockFromItem(wood.getItem());
 						return block.getStateFromMeta(wood.getMetadata()).getBlockHardness(world, pos);
 					}
@@ -593,14 +601,12 @@ public abstract class BlockPile extends BlockStructure implements ITileEntityPro
 		}
 		return super.getBlockHardness(blockState, world, pos);
 	}
-	
-	public static ItemStack createWoodPile(ITree tree) {
-		if (tree != null) {
+
+	public static ItemStack createWoodPile(IAlleleTreeSpecies treeSpecies) {
+		if (treeSpecies != null) {
 			ItemStack stack = new ItemStack(PluginArboriculture.blocks.piles.get(EnumPileType.WOOD));
-			NBTTagCompound nbtTag = new NBTTagCompound();
-			tree.writeToNBT(nbtTag);
 			NBTTagCompound nbtItem = new NBTTagCompound();
-			nbtItem.setTag("ContainedTree", nbtTag);
+			nbtItem.setString("TreeSpecies", treeSpecies.getUID());
 			stack.setTagCompound(nbtItem);
 			return stack;
 		}

src/main/java/forestry/arboriculture/commands/TreeModeHelper.java

@@ -13,17 +13,16 @@ package forestry.arboriculture.commands;
 import java.util.ArrayList;
 import java.util.List;
 
-import net.minecraft.world.World;
-
 import forestry.api.arboriculture.ITreekeepingMode;
 import forestry.api.arboriculture.TreeManager;
 import forestry.core.commands.ICommandModeHelper;
+import net.minecraft.world.World;
 
 public class TreeModeHelper implements ICommandModeHelper {
 
 	@Override
 	public String[] getModeNames() {
-		ArrayList<ITreekeepingMode> treekeepingModes = TreeManager.treeRoot.getTreekeepingModes();
+		List<ITreekeepingMode> treekeepingModes = TreeManager.treeRoot.getTreekeepingModes();
 		int modeStringCount = treekeepingModes.size();
 		List<String> modeStrings = new ArrayList<>(modeStringCount);
 		for (ITreekeepingMode mode : treekeepingModes) {

src/main/java/forestry/arboriculture/genetics/GrowthProvider.java

@@ -11,47 +11,23 @@
 package forestry.arboriculture.genetics;
 
 import javax.annotation.Nullable;
-import java.util.HashMap;
-import java.util.Map;
 
-import net.minecraft.block.state.IBlockState;
+import forestry.api.arboriculture.IGrowthProvider;
+import forestry.api.arboriculture.ITreeGenome;
+import forestry.core.utils.Translator;
 import net.minecraft.util.math.BlockPos;
-import net.minecraft.util.math.Vec3i;
 import net.minecraft.world.World;
 
-import forestry.api.arboriculture.EnumGrowthConditions;
-import forestry.api.arboriculture.IGrowthProvider;
-import forestry.api.arboriculture.ITree;
-import forestry.api.arboriculture.ITreeGenome;
-import forestry.api.core.ForestryAPI;
-import forestry.arboriculture.tiles.TileSapling;
-import forestry.core.tiles.TileUtil;
-import forestry.core.utils.Translator;
-
+/**
+ * @deprecated this is being removed to simplify trees
+ */
+@Deprecated
 public class GrowthProvider implements IGrowthProvider {
 
 	@Override
 	@Nullable
 	public BlockPos canGrow(ITreeGenome genome, World world, BlockPos pos, int expectedGirth, int expectedHeight) {
-		BlockPos growthPos = hasSufficientSaplingsAroundSapling(genome, world, pos, expectedGirth);
-		if (growthPos == null) {
-			return null;
-		}
-
-		if (!hasRoom(world, growthPos, expectedGirth, expectedHeight)) {
-			return null;
-		}
-
-		if (getGrowthConditions(genome, world, growthPos) == EnumGrowthConditions.HOSTILE) {
-			return null;
-		}
-
-		return growthPos;
-	}
-
-	@Override
-	public EnumGrowthConditions getGrowthConditions(ITreeGenome genome, World world, BlockPos pos) {
-		return getConditionFromLight(world, pos);
+		return TreeGrowthHelper.canGrow(world, genome, pos, expectedGirth, expectedHeight);
 	}
 
 	@Override
@@ -63,118 +39,4 @@ public class GrowthProvider implements IGrowthProvider {
 	public String[] getInfo() {
 		return new String[0];
 	}
-
-	protected static EnumGrowthConditions getConditionsFromRainfall(World world, BlockPos pos, float min, float max) {
-		float humidity = ForestryAPI.climateManager.getHumidity(world, pos);
-		
-		if (humidity < min || humidity > max) {
-			return EnumGrowthConditions.HOSTILE;
-		}
-
-		return EnumGrowthConditions.EXCELLENT;
-	}
-
-	protected static EnumGrowthConditions getConditionsFromTemperature(World world, BlockPos pos, float min, float max) {
-		float biomeTemperature = ForestryAPI.climateManager.getTemperature(world, pos);
-		if (biomeTemperature < min || biomeTemperature > max) {
-			return EnumGrowthConditions.HOSTILE;
-		}
-
-		return EnumGrowthConditions.EXCELLENT;
-	}
-
-	protected static EnumGrowthConditions getConditionFromLight(World world, BlockPos pos) {
-		int lightValue = world.getLightFromNeighbors(pos.up());
-
-		if (lightValue > 13) {
-			return EnumGrowthConditions.EXCELLENT;
-		} else if (lightValue > 11) {
-			return EnumGrowthConditions.GOOD;
-		} else if (lightValue > 8) {
-			return EnumGrowthConditions.NORMAL;
-		} else if (lightValue > 6) {
-			return EnumGrowthConditions.PALTRY;
-		} else {
-			return EnumGrowthConditions.HOSTILE;
-		}
-	}
-
-	private static boolean hasRoom(World world, BlockPos pos, int expectedGirth, int expectedHeight) {
-		Vec3i area = new Vec3i(expectedGirth, expectedHeight + 1, expectedGirth);
-		return checkArea(world, pos.up(), area);
-	}
-
-	private static boolean checkArea(World world, BlockPos start, Vec3i area) {
-		for (int x = 0; x < area.getX(); x++) {
-			for (int y = 0; y < area.getY(); y++) {
-				for (int z = 0; z < area.getZ(); z++) {
-					BlockPos pos = start.add(x, y, z);
-					IBlockState blockState = world.getBlockState(pos);
-					if (!blockState.getBlock().isReplaceable(world, pos)) {
-						return false;
-					}
-				}
-			}
-		}
-		return true;
-	}
-
-	/**
-	 * Checks an area for saplings.
-	 * If saplings need to be 2x2, 3x3, etc, it will check all configurations in which pos is included in that area.
-	 * Uses a knownSaplings cache to avoid checking the same saplings multiple times.
-	 */
-	@Nullable
-	private static BlockPos hasSufficientSaplingsAroundSapling(ITreeGenome genome, World world, BlockPos saplingPos, int expectedGirth) {
-		final int checkSize = (expectedGirth * 2) - 1;
-		final int offset = expectedGirth - 1;
-		final Map<BlockPos, Boolean> knownSaplings = new HashMap<>(checkSize * checkSize);
-
-		for (int x = -offset; x <= 0; x++) {
-			for (int z = -offset; z <= 0; z++) {
-				BlockPos startPos = saplingPos.add(x, 0, z);
-				if (checkForSaplings(genome, world, startPos, expectedGirth, knownSaplings)) {
-					return startPos;
-				}
-			}
-		}
-
-		return null;
-	}
-
-	private static boolean checkForSaplings(ITreeGenome genome, World world, BlockPos startPos, int girth, Map<BlockPos, Boolean> knownSaplings) {
-		for (int x = 0; x < girth; x++) {
-			for (int z = 0; z < girth; z++) {
-				BlockPos checkPos = startPos.add(x, 0, z);
-				Boolean knownSapling = knownSaplings.get(checkPos);
-				if (knownSapling == null) {
-					knownSapling = isSapling(genome, world, checkPos);
-					knownSaplings.put(checkPos, knownSapling);
-				}
-
-				if (!knownSapling) {
-					return false;
-				}
-			}
-		}
-		return true;
-	}
-
-	private static boolean isSapling(ITreeGenome genome, World world, BlockPos pos) {
-		if (!world.isBlockLoaded(pos)) {
-			return false;
-		}
-
-		if (world.isAirBlock(pos)) {
-			return false;
-		}
-
-		TileSapling sapling = TileUtil.getTile(world, pos, TileSapling.class);
-		if (sapling == null) {
-			return false;
-		}
-
-		ITree tree = sapling.getTree();
-		return tree != null && tree.getGenome().getPrimary().getUID().equals(genome.getPrimary().getUID());
-	}
 }

src/main/java/forestry/arboriculture/genetics/GrowthProviderTropical.java

@@ -1,54 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2011-2014 SirSengir.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the GNU Lesser Public License v3
- * which accompanies this distribution, and is available at
- * http://www.gnu.org/licenses/lgpl-3.0.txt
- *
- * Various Contributors including, but not limited to:
- * SirSengir (original work), CovertJaguar, Player, Binnie, MysteriousAges
- ******************************************************************************/
-package forestry.arboriculture.genetics;
-
-import java.util.EnumSet;
-
-import net.minecraft.init.Biomes;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-import forestry.api.arboriculture.EnumGrowthConditions;
-import forestry.api.arboriculture.ITreeGenome;
-import forestry.core.utils.Translator;
-
-public class GrowthProviderTropical extends GrowthProvider {
-
-	@Override
-	public EnumGrowthConditions getGrowthConditions(ITreeGenome genome, World world, BlockPos pos) {
-		EnumGrowthConditions light = getConditionFromLight(world, pos);
-		EnumGrowthConditions moisture = getConditionsFromRainfall(world, pos, Biomes.JUNGLE.getRainfall(), 2.0f);
-
-		float jungleTemperature = Biomes.JUNGLE.getFloatTemperature(pos);
-		float desertTemperature = Biomes.DESERT.getFloatTemperature(pos);
-		EnumGrowthConditions temperature = getConditionsFromTemperature(world, pos, jungleTemperature, desertTemperature - 0.1f);
-
-		EnumSet<EnumGrowthConditions> conditions = EnumSet.of(light, moisture, temperature);
-
-		EnumGrowthConditions result = EnumGrowthConditions.HOSTILE;
-		for (EnumGrowthConditions cond : conditions) {
-			if (cond == EnumGrowthConditions.HOSTILE) {
-				return EnumGrowthConditions.HOSTILE;
-			}
-
-			if (cond.ordinal() > result.ordinal()) {
-				result = cond;
-			}
-		}
-
-		return result;
-	}
-
-	@Override
-	public String getDescription() {
-		return Translator.translateToLocal("for.growth.tropical");
-	}
-
-}

src/main/java/forestry/arboriculture/genetics/Tree.java

@@ -14,34 +14,16 @@ import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.EnumSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Random;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.util.EnumFacing;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.util.text.TextFormatting;
-import net.minecraft.world.IBlockAccess;
-import net.minecraft.world.World;
-import net.minecraft.world.gen.feature.WorldGenerator;
-
 import com.mojang.authlib.GameProfile;
-
-import net.minecraftforge.common.EnumPlantType;
-import net.minecraftforge.common.IPlantable;
-
-import forestry.api.arboriculture.EnumGrowthConditions;
 import forestry.api.arboriculture.EnumTreeChromosome;
 import forestry.api.arboriculture.IAlleleLeafEffect;
 import forestry.api.arboriculture.IAlleleTreeSpecies;
 import forestry.api.arboriculture.IArboristTracker;
 import forestry.api.arboriculture.IFruitProvider;
-import forestry.api.arboriculture.IGrowthProvider;
 import forestry.api.arboriculture.ITree;
 import forestry.api.arboriculture.ITreeGenome;
 import forestry.api.arboriculture.ITreeMutation;
@@ -57,6 +39,18 @@ import forestry.core.config.Config;
 import forestry.core.genetics.Chromosome;
 import forestry.core.genetics.Individual;
 import forestry.core.utils.Translator;
+import net.minecraft.block.Block;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.util.EnumFacing;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.util.text.TextFormatting;
+import net.minecraft.world.IBlockAccess;
+import net.minecraft.world.World;
+import net.minecraft.world.gen.feature.WorldGenerator;
+import net.minecraftforge.common.EnumPlantType;
+import net.minecraftforge.common.IPlantable;
 
 public class Tree extends Individual implements ITree, IPlantable {
 
@@ -65,13 +59,8 @@ public class Tree extends Individual implements ITree, IPlantable {
 	@Nullable
 	private ITreeGenome mate;
 
-	private final EnumSet<EnumPlantType> plantTypes;
-	private EnumPlantType plantType;
-
 	public Tree(@Nonnull ITreeGenome genome) {
 		this.genome = genome;
-		plantTypes = genome.getPlantTypes();
-		plantTypes.add(genome.getPrimary().getPlantType());
 	}
 
 	public Tree(@Nonnull NBTTagCompound nbttagcompound) {
@@ -83,9 +72,6 @@ public class Tree extends Individual implements ITree, IPlantable {
 			this.genome = TreeDefinition.Oak.getGenome();
 		}
 
-		this.plantTypes = genome.getPlantTypes();
-		this.plantTypes.add(genome.getPrimary().getPlantType());
-
 		if (nbttagcompound.hasKey("Mate")) {
 			mate = new TreeGenome(nbttagcompound.getCompoundTag("Mate"));
 		}
@@ -164,12 +150,8 @@ public class Tree extends Individual implements ITree, IPlantable {
 		}
 
 		Block block = blockState.getBlock();
-
-		for (EnumPlantType type : getPlantTypes()) {
-			this.plantType = type;
-			if (block.canSustainPlant(blockState, world, blockPos, EnumFacing.UP, this)) {
-				return true;
-			}
+		if (block.canSustainPlant(blockState, world, blockPos, EnumFacing.UP, this)) {
+			return true;
 		}
 
 		return false;
@@ -177,7 +159,7 @@ public class Tree extends Individual implements ITree, IPlantable {
 
 	@Override
 	public EnumPlantType getPlantType(IBlockAccess world, BlockPos pos) {
-		return plantType;
+		return genome.getPrimary().getPlantType();
 	}
 
 	@Override
@@ -188,8 +170,7 @@ public class Tree extends Individual implements ITree, IPlantable {
 	@Override
 	@Nullable
 	public BlockPos canGrow(World world, BlockPos pos, int expectedGirth, int expectedHeight) {
-		IGrowthProvider growthProvider = genome.getGrowthProvider();
-		return growthProvider.canGrow(genome, world, pos, expectedGirth, expectedHeight);
+		return TreeGrowthHelper.canGrow(world, genome, pos, expectedGirth, expectedHeight);
 	}
 
 	@Override
@@ -197,11 +178,6 @@ public class Tree extends Individual implements ITree, IPlantable {
 		return genome.getMaturationTime();
 	}
 
-	@Override
-	public EnumGrowthConditions getGrowthCondition(World world, BlockPos pos) {
-		return genome.getGrowthProvider().getGrowthConditions(getGenome(), world, pos);
-	}
-
 	@Override
 	public int getGirth() {
 		return genome.getGirth();
@@ -275,11 +251,6 @@ public class Tree extends Individual implements ITree, IPlantable {
 		return genome.getActiveAllele(chromosome).getUID().equals(genome.getInactiveAllele(chromosome).getUID());
 	}
 
-	@Override
-	public EnumSet<EnumPlantType> getPlantTypes() {
-		return plantTypes;
-	}
-
 	@Override
 	public void addTooltip(List<String> list) {
 
@@ -302,8 +273,8 @@ public class Tree extends Individual implements ITree, IPlantable {
 		String girth = TextFormatting.AQUA + "G: " + String.format("%sx%s", genome.getGirth(), genome.getGirth());
 		String saplings = TextFormatting.YELLOW + "S: " + genome.getActiveAllele(EnumTreeChromosome.FERTILITY).getName();
 		String yield = TextFormatting.WHITE + "Y: " + genome.getActiveAllele(EnumTreeChromosome.YIELD).getName();
-		String combustibility = TextFormatting.DARK_GRAY + "CO: " + genome.getCombustibility();
-		String carbonization = TextFormatting.GRAY + "CA: " + genome.getCarbonization();
+		String combustibility = TextFormatting.DARK_GRAY + "CO: " + primary.getWoodProvider().getCombustibility();
+		String carbonization = TextFormatting.GRAY + "CA: " + secondary.getWoodProvider().getCarbonization();
 		list.add(String.format("%s, %s", saplings, maturation));
 		list.add(String.format("%s, %s", height, girth));
 		list.add(String.format("%s, %s", yield, sappiness));

src/main/java/forestry/arboriculture/genetics/TreeAlyzerPlugin.java

@@ -11,23 +11,14 @@
 package forestry.arboriculture.genetics;
 
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 
-import net.minecraft.item.ItemStack;
-import net.minecraft.util.text.TextFormatting;
-
-import net.minecraftforge.common.EnumPlantType;
-import net.minecraftforge.fml.relauncher.Side;
-import net.minecraftforge.fml.relauncher.SideOnly;
-
 import forestry.api.arboriculture.EnumGermlingType;
 import forestry.api.arboriculture.EnumTreeChromosome;
 import forestry.api.arboriculture.IAlleleFruit;
-import forestry.api.arboriculture.IAlleleGrowth;
 import forestry.api.arboriculture.IAlleleTreeSpecies;
 import forestry.api.arboriculture.ITree;
 import forestry.api.arboriculture.TreeManager;
@@ -38,13 +29,16 @@ import forestry.api.genetics.IFruitFamily;
 import forestry.arboriculture.PluginArboriculture;
 import forestry.arboriculture.genetics.alleles.AlleleFruit;
 import forestry.core.config.Config;
-import forestry.core.genetics.alleles.AllelePlantType;
 import forestry.core.gui.GuiAlyzer;
 import forestry.core.gui.TextLayoutHelper;
 import forestry.core.gui.widgets.ItemStackWidget;
 import forestry.core.gui.widgets.WidgetManager;
 import forestry.core.proxy.Proxies;
 import forestry.core.utils.Translator;
+import net.minecraft.item.ItemStack;
+import net.minecraft.util.text.TextFormatting;
+import net.minecraftforge.fml.relauncher.Side;
+import net.minecraftforge.fml.relauncher.SideOnly;
 
 public class TreeAlyzerPlugin implements IAlyzerPlugin {
 	public static final TreeAlyzerPlugin INSTANCE = new TreeAlyzerPlugin();
@@ -110,12 +104,6 @@ public class TreeAlyzerPlugin implements IAlyzerPlugin {
 		textLayout.newLineCompressed();
 
 		gui.drawChromosomeRow(Translator.translateToLocal("for.gui.effect"), tree, EnumTreeChromosome.EFFECT);
-		textLayout.newLineCompressed();
-		IAlleleInteger activeCombustibility = (IAlleleInteger) tree.getGenome().getActiveAllele(EnumTreeChromosome.COMBUSTIBILITY);
-		IAlleleInteger inactiveCombustibility = (IAlleleInteger) tree.getGenome().getInactiveAllele(EnumTreeChromosome.COMBUSTIBILITY);
-		textLayout.drawLine(Translator.translateToLocal("for.gui.combustibility"), GuiAlyzer.COLUMN_0);
-		gui.drawLine(Integer.toString(activeCombustibility.getValue()), GuiAlyzer.COLUMN_1, tree, EnumTreeChromosome.COMBUSTIBILITY, false);
-		gui.drawLine(Integer.toString(inactiveCombustibility.getValue()), GuiAlyzer.COLUMN_2, tree, EnumTreeChromosome.COMBUSTIBILITY, true);
 
 		textLayout.endPage();
 	}
@@ -140,20 +128,24 @@ public class TreeAlyzerPlugin implements IAlyzerPlugin {
 
 		textLayout.newLine();
 		textLayout.newLine();
-		
-		IAlleleInteger activeCarbonization = (IAlleleInteger) tree.getGenome().getActiveAllele(EnumTreeChromosome.CARBONIZATION);
-		IAlleleInteger inactiveCarbonization = (IAlleleInteger) tree.getGenome().getInactiveAllele(EnumTreeChromosome.CARBONIZATION);
+
+		IAlleleTreeSpecies activeSpecies = (IAlleleTreeSpecies) tree.getGenome().getActiveAllele(EnumTreeChromosome.SPECIES);
+		IAlleleTreeSpecies inActiveSpecies = (IAlleleTreeSpecies) tree.getGenome().getInactiveAllele(EnumTreeChromosome.SPECIES);
+
+		int activeCombustibility = activeSpecies.getWoodProvider().getCombustibility();
+		int inactiveCombustibility = inActiveSpecies.getWoodProvider().getCombustibility();
+		textLayout.drawLine(Translator.translateToLocal("for.gui.combustibility"), GuiAlyzer.COLUMN_0);
+		gui.drawLine(Integer.toString(activeCombustibility), GuiAlyzer.COLUMN_1, tree, EnumTreeChromosome.SPECIES, false);
+		gui.drawLine(Integer.toString(inactiveCombustibility), GuiAlyzer.COLUMN_2, tree, EnumTreeChromosome.SPECIES, true);
+
+		textLayout.newLineCompressed();
+
+		int activeCarbonization = activeSpecies.getWoodProvider().getCarbonization();
+		int inactiveCarbonization = inActiveSpecies.getWoodProvider().getCarbonization();
 		textLayout.drawLine(Translator.translateToLocal("for.gui.carbonization"), GuiAlyzer.COLUMN_0);
-		gui.drawLine(Integer.toString(activeCarbonization.getValue()), GuiAlyzer.COLUMN_1, tree, EnumTreeChromosome.CARBONIZATION, false);
-		gui.drawLine(Integer.toString(inactiveCarbonization.getValue()), GuiAlyzer.COLUMN_2, tree, EnumTreeChromosome.CARBONIZATION, true);
-		textLayout.newLineCompressed();
-
-		textLayout.drawLine(Translator.translateToLocal("for.gui.growth"), GuiAlyzer.COLUMN_0);
-		gui.drawLine(tree.getGenome().getGrowthProvider().getDescription(), GuiAlyzer.COLUMN_1, tree, EnumTreeChromosome.GROWTH, false);
-		gui.drawLine(((IAlleleGrowth) tree.getGenome().getInactiveAllele(EnumTreeChromosome.GROWTH)).getProvider().getDescription(), GuiAlyzer.COLUMN_2, tree,
-				EnumTreeChromosome.GROWTH, true);
-
-		textLayout.newLineCompressed();
+		gui.drawLine(Integer.toString(activeCarbonization), GuiAlyzer.COLUMN_1, tree, EnumTreeChromosome.SPECIES, false);
+		gui.drawLine(Integer.toString(inactiveCarbonization), GuiAlyzer.COLUMN_2, tree, EnumTreeChromosome.SPECIES, true);
+		textLayout.newLine();
 
 		textLayout.drawLine(Translator.translateToLocal("for.gui.native"), GuiAlyzer.COLUMN_0);
 		textLayout.drawLine(Translator.translateToLocal("for.gui." + tree.getGenome().getPrimary().getPlantType().toString().toLowerCase(Locale.ENGLISH)), GuiAlyzer.COLUMN_1,
@@ -161,38 +153,14 @@ public class TreeAlyzerPlugin implements IAlyzerPlugin {
 		textLayout.drawLine(Translator.translateToLocal("for.gui." + tree.getGenome().getSecondary().getPlantType().toString().toLowerCase(Locale.ENGLISH)), GuiAlyzer.COLUMN_2,
 				speciesDominance1);
 
-		textLayout.newLineCompressed();
-
-		textLayout.drawLine(Translator.translateToLocal("for.gui.tolerated"), GuiAlyzer.COLUMN_0);
-
-		List<EnumPlantType> activeTolerated = new ArrayList<>(tree.getGenome().getPlantTypes());
-		List<EnumPlantType> inactiveTolerated = Collections.emptyList();
-
-		IAllele inactiveAllelePlant = tree.getGenome().getInactiveAllele(EnumTreeChromosome.PLANT);
-		if (inactiveAllelePlant instanceof AllelePlantType) {
-			inactiveTolerated = new ArrayList<>(((AllelePlantType) inactiveAllelePlant).getPlantTypes());
-		}
-
-		int max = Math.max(activeTolerated.size(), inactiveTolerated.size());
-		for (int i = 0; i < max; i++) {
-			if (i > 0) {
-				textLayout.newLineCompressed();
-			}
-			if (activeTolerated.size() > i) {
-				gui.drawLine(Translator.translateToLocal("for.gui." + activeTolerated.get(i).toString().toLowerCase(Locale.ENGLISH)), GuiAlyzer.COLUMN_1, tree, EnumTreeChromosome.PLANT, false);
-			}
-			if (inactiveTolerated.size() > i) {
-				gui.drawLine(Translator.translateToLocal("for.gui." + inactiveTolerated.get(i).toString().toLowerCase(Locale.ENGLISH)), GuiAlyzer.COLUMN_2, tree, EnumTreeChromosome.PLANT, true);
-			}
-		}
-		textLayout.newLineCompressed();
+		textLayout.newLine();
 
 		// FRUITS
 		textLayout.drawLine(Translator.translateToLocal("for.gui.supports"), GuiAlyzer.COLUMN_0);
 		List<IFruitFamily> families0 = new ArrayList<>(tree.getGenome().getPrimary().getSuitableFruit());
 		List<IFruitFamily> families1 = new ArrayList<>(tree.getGenome().getSecondary().getSuitableFruit());
 
-		max = Math.max(families0.size(), families1.size());
+		int max = Math.max(families0.size(), families1.size());
 		for (int i = 0; i < max; i++) {
 			if (i > 0) {
 				textLayout.newLineCompressed();
@@ -206,8 +174,7 @@ public class TreeAlyzerPlugin implements IAlyzerPlugin {
 			}
 
 		}
-		
-		textLayout.newLine();
+
 		textLayout.newLine();
 
 		int fruitDominance0 = gui.getColorCoding(tree.getGenome().getActiveAllele(EnumTreeChromosome.FRUITS).isDominant());

src/main/java/forestry/arboriculture/genetics/TreeDefinition.java

@@ -10,22 +10,11 @@
  ******************************************************************************/
 package forestry.arboriculture.genetics;
 
-import java.awt.Color;
+import java.awt.*;
 import java.util.Arrays;
 import java.util.Locale;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.BlockLog;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.item.ItemStack;
-import net.minecraft.util.EnumFacing;
-import net.minecraft.util.IStringSerializable;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-import net.minecraft.world.gen.feature.WorldGenerator;
-
 import com.mojang.authlib.GameProfile;
-
 import forestry.api.arboriculture.EnumForestryWoodType;
 import forestry.api.arboriculture.EnumFruitFamily;
 import forestry.api.arboriculture.EnumGermlingType;
@@ -50,7 +39,6 @@ import forestry.api.genetics.IAllele;
 import forestry.api.world.ITreeGenData;
 import forestry.arboriculture.PluginArboriculture;
 import forestry.arboriculture.genetics.alleles.AlleleFruit;
-import forestry.arboriculture.genetics.alleles.AlleleGrowth;
 import forestry.arboriculture.models.ModelProviderFactory;
 import forestry.arboriculture.tiles.TileLeaves;
 import forestry.arboriculture.worldgen.WorldGenAcacia;
@@ -94,6 +82,15 @@ import forestry.core.genetics.alleles.AlleleHelper;
 import forestry.core.genetics.alleles.AllelePlantType;
 import forestry.core.genetics.alleles.EnumAllele;
 import forestry.core.tiles.TileUtil;
+import net.minecraft.block.Block;
+import net.minecraft.block.BlockLog;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.item.ItemStack;
+import net.minecraft.util.EnumFacing;
+import net.minecraft.util.IStringSerializable;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
+import net.minecraft.world.gen.feature.WorldGenerator;
 
 public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSerializable {
 	Oak(TreeBranchDefinition.QUERCUS, "appleOak", "robur", false, EnumLeafType.DECIDUOUS, new Color(4764952), new Color(4764952).brighter(), EnumVanillaWoodType.OAK) {
@@ -107,8 +104,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FRUITS, AlleleFruit.fruitApple);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FERTILITY, EnumAllele.Saplings.AVERAGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.FASTER);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.CARBONIZATION, 5);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 20);
 		}
 
 		@Override
@@ -132,8 +127,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FERTILITY, EnumAllele.Saplings.AVERAGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.FASTER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.GIRTH, 2);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.CARBONIZATION, 5);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 20);
 		}
 
 		@Override
@@ -156,7 +149,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 		protected void setAlleles(IAllele[] alleles) {
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FERTILITY, EnumAllele.Saplings.AVERAGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.FASTER);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 19);
 		}
 
 		@Override
@@ -180,7 +172,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FERTILITY, EnumAllele.Saplings.LOW);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOWER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.YIELD, EnumAllele.Yield.LOWER);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 19);
 			//Allele.helper.set(alleles, EnumTreeChromosome.EFFECT, Allele.leavesBrimstone);
 		}
 
@@ -217,7 +208,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOWER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.HEIGHT, EnumAllele.Height.AVERAGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.GIRTH, 2);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 21);
 		}
 
 		@Override
@@ -245,7 +235,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOWER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.HEIGHT, EnumAllele.Height.LARGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.GIRTH, 2);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 21);
 		}
 
 		@Override
@@ -348,7 +337,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FERTILITY, EnumAllele.Saplings.LOW);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOWER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.HEIGHT, EnumAllele.Height.AVERAGE);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 20);
 		}
 
 		@Override
@@ -372,7 +360,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FERTILITY, EnumAllele.Saplings.AVERAGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.HEIGHT, EnumAllele.Height.AVERAGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.FASTER);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 19);
 		}
 
 		@Override
@@ -396,7 +383,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FERTILITY, EnumAllele.Saplings.LOW);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOWER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.HEIGHT, EnumAllele.Height.AVERAGE);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 20);
 		}
 
 		@Override
@@ -470,8 +456,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOWEST);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.SLOWEST);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.GIRTH, 4);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.CARBONIZATION, 3);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 18);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FIREPROOF, EnumAllele.Fireproof.TRUE);
 		}
 
@@ -496,7 +480,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.FRUITS, AlleleFruit.fruitCocoa);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.HEIGHT, EnumAllele.Height.LARGER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.FAST);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.CARBONIZATION, 5);
 		}
 
 		@Override
@@ -590,7 +573,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOW);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.SLOWER);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.GIRTH, 3);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 20);
 		}
 
 		@Override
@@ -658,7 +640,7 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 
 		@Override
 		protected void setAlleles(IAllele[] alleles) {
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 20);
+
 		}
 
 		@Override
@@ -681,7 +663,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 		@Override
 		protected void setAlleles(IAllele[] alleles) {
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.PLANT, AllelePlantType.plantTypeDesert);
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.COMBUSTIBILITY, 20);
 		}
 
 		@Override
@@ -876,7 +857,6 @@ public enum TreeDefinition implements ITreeDefinition, ITreeGenerator, IStringSe
 
 		@Override
 		protected void setAlleles(IAllele[] alleles) {
-			AlleleHelper.instance.set(alleles, EnumTreeChromosome.GROWTH, AlleleGrowth.growthTropical);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.HEIGHT, EnumAllele.Height.LARGE);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.SAPPINESS, EnumAllele.Sappiness.LOW);
 			AlleleHelper.instance.set(alleles, EnumTreeChromosome.MATURATION, EnumAllele.Maturation.SLOW);

src/main/java/forestry/arboriculture/genetics/TreeGenome.java

@@ -11,20 +11,12 @@
 package forestry.arboriculture.genetics;
 
 import javax.annotation.Nonnull;
-import java.util.EnumSet;
-
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-
-import net.minecraftforge.common.EnumPlantType;
 
 import forestry.api.arboriculture.EnumTreeChromosome;
 import forestry.api.arboriculture.IAlleleFruit;
-import forestry.api.arboriculture.IAlleleGrowth;
 import forestry.api.arboriculture.IAlleleLeafEffect;
 import forestry.api.arboriculture.IAlleleTreeSpecies;
 import forestry.api.arboriculture.IFruitProvider;
-import forestry.api.arboriculture.IGrowthProvider;
 import forestry.api.arboriculture.ITreeGenome;
 import forestry.api.arboriculture.TreeManager;
 import forestry.api.genetics.IAlleleFloat;
@@ -33,7 +25,8 @@ import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IChromosome;
 import forestry.api.genetics.ISpeciesRoot;
 import forestry.core.genetics.Genome;
-import forestry.core.genetics.alleles.AllelePlantType;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
 
 public class TreeGenome extends Genome implements ITreeGenome {
 
@@ -51,7 +44,7 @@ public class TreeGenome extends Genome implements ITreeGenome {
 			return null;
 		}
 
-		IAlleleSpecies species = getSpeciesDirectly(itemStack);
+		IAlleleSpecies species = getSpeciesDirectly(TreeManager.treeRoot, itemStack);
 		if (species instanceof IAlleleTreeSpecies) {
 			return (IAlleleTreeSpecies) species;
 		}
@@ -75,11 +68,6 @@ public class TreeGenome extends Genome implements ITreeGenome {
 		return ((IAlleleFruit) getActiveAllele(EnumTreeChromosome.FRUITS)).getProvider();
 	}
 
-	@Override
-	public IGrowthProvider getGrowthProvider() {
-		return ((IAlleleGrowth) getActiveAllele(EnumTreeChromosome.GROWTH)).getProvider();
-	}
-
 	@Override
 	public float getHeight() {
 		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.HEIGHT)).getValue();
@@ -100,11 +88,6 @@ public class TreeGenome extends Genome implements ITreeGenome {
 		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.SAPPINESS)).getValue();
 	}
 
-	@Override
-	public EnumSet<EnumPlantType> getPlantTypes() {
-		return ((AllelePlantType) getActiveAllele(EnumTreeChromosome.PLANT)).getPlantTypes();
-	}
-
 	@Override
 	public int getMaturationTime() {
 		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.MATURATION)).getValue();
@@ -115,16 +98,6 @@ public class TreeGenome extends Genome implements ITreeGenome {
 		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.GIRTH)).getValue();
 	}
 	
-	@Override
-	public int getCombustibility(){
-		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.COMBUSTIBILITY)).getValue();
-	}
-	
-	@Override
-	public int getCarbonization(){
-		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.CARBONIZATION)).getValue();
-	}
-	
 	@Override
 	public IAlleleLeafEffect getEffect() {
 		return (IAlleleLeafEffect) getActiveAllele(EnumTreeChromosome.EFFECT);

src/main/java/forestry/arboriculture/genetics/TreeGrowthHelper.java

@@ -0,0 +1,109 @@
+package forestry.arboriculture.genetics;
+
+import javax.annotation.Nullable;
+import java.util.HashMap;
+import java.util.Map;
+
+import forestry.api.arboriculture.ITree;
+import forestry.api.arboriculture.ITreeGenome;
+import forestry.arboriculture.tiles.TileSapling;
+import forestry.core.tiles.TileUtil;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.util.math.Vec3i;
+import net.minecraft.world.World;
+
+public class TreeGrowthHelper {
+	@Nullable
+	public static BlockPos canGrow(World world, ITreeGenome genome, BlockPos pos, int expectedGirth, int expectedHeight) {
+		BlockPos growthPos = hasSufficientSaplingsAroundSapling(genome, world, pos, expectedGirth);
+		if (growthPos == null) {
+			return null;
+		}
+
+		if (!hasRoom(world, growthPos, expectedGirth, expectedHeight)) {
+			return null;
+		}
+
+		return growthPos;
+	}
+
+	private static boolean hasRoom(World world, BlockPos pos, int expectedGirth, int expectedHeight) {
+		Vec3i area = new Vec3i(expectedGirth, expectedHeight + 1, expectedGirth);
+		return checkArea(world, pos.up(), area);
+	}
+
+	private static boolean checkArea(World world, BlockPos start, Vec3i area) {
+		for (int x = 0; x < area.getX(); x++) {
+			for (int y = 0; y < area.getY(); y++) {
+				for (int z = 0; z < area.getZ(); z++) {
+					BlockPos pos = start.add(x, y, z);
+					IBlockState blockState = world.getBlockState(pos);
+					if (!blockState.getBlock().isReplaceable(world, pos)) {
+						return false;
+					}
+				}
+			}
+		}
+		return true;
+	}
+
+	/**
+	 * Checks an area for saplings.
+	 * If saplings need to be 2x2, 3x3, etc, it will check all configurations in which pos is included in that area.
+	 * Uses a knownSaplings cache to avoid checking the same saplings multiple times.
+	 */
+	@Nullable
+	private static BlockPos hasSufficientSaplingsAroundSapling(ITreeGenome genome, World world, BlockPos saplingPos, int expectedGirth) {
+		final int checkSize = (expectedGirth * 2) - 1;
+		final int offset = expectedGirth - 1;
+		final Map<BlockPos, Boolean> knownSaplings = new HashMap<>(checkSize * checkSize);
+
+		for (int x = -offset; x <= 0; x++) {
+			for (int z = -offset; z <= 0; z++) {
+				BlockPos startPos = saplingPos.add(x, 0, z);
+				if (checkForSaplings(genome, world, startPos, expectedGirth, knownSaplings)) {
+					return startPos;
+				}
+			}
+		}
+
+		return null;
+	}
+
+	private static boolean checkForSaplings(ITreeGenome genome, World world, BlockPos startPos, int girth, Map<BlockPos, Boolean> knownSaplings) {
+		for (int x = 0; x < girth; x++) {
+			for (int z = 0; z < girth; z++) {
+				BlockPos checkPos = startPos.add(x, 0, z);
+				Boolean knownSapling = knownSaplings.get(checkPos);
+				if (knownSapling == null) {
+					knownSapling = isSapling(genome, world, checkPos);
+					knownSaplings.put(checkPos, knownSapling);
+				}
+
+				if (!knownSapling) {
+					return false;
+				}
+			}
+		}
+		return true;
+	}
+
+	private static boolean isSapling(ITreeGenome genome, World world, BlockPos pos) {
+		if (!world.isBlockLoaded(pos)) {
+			return false;
+		}
+
+		if (world.isAirBlock(pos)) {
+			return false;
+		}
+
+		TileSapling sapling = TileUtil.getTile(world, pos, TileSapling.class);
+		if (sapling == null) {
+			return false;
+		}
+
+		ITree tree = sapling.getTree();
+		return tree != null && tree.getGenome().getPrimary().getUID().equals(genome.getPrimary().getUID());
+	}
+}

src/main/java/forestry/arboriculture/genetics/TreeRoot.java

@@ -18,23 +18,7 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map.Entry;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.BlockHorizontal;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.init.Blocks;
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.tileentity.TileEntity;
-import net.minecraft.util.EnumFacing;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
 import com.mojang.authlib.GameProfile;
-
-import net.minecraftforge.fml.common.FMLCommonHandler;
-import net.minecraftforge.oredict.OreDictionary;
-
 import forestry.api.arboriculture.EnumGermlingType;
 import forestry.api.arboriculture.EnumTreeChromosome;
 import forestry.api.arboriculture.IAlleleFruit;
@@ -65,6 +49,19 @@ import forestry.core.proxy.Proxies;
 import forestry.core.tiles.TileUtil;
 import forestry.core.utils.BlockUtil;
 import forestry.core.utils.GeneticsUtil;
+import net.minecraft.block.Block;
+import net.minecraft.block.BlockHorizontal;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.init.Blocks;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.tileentity.TileEntity;
+import net.minecraft.util.EnumFacing;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
+import net.minecraftforge.fml.common.FMLCommonHandler;
+import net.minecraftforge.oredict.OreDictionary;
 
 public class TreeRoot extends SpeciesRoot implements ITreeRoot {
 
@@ -423,7 +420,7 @@ public class TreeRoot extends SpeciesRoot implements ITreeRoot {
 	}
 
 	@Override
-	public IChromosomeType getKaryotypeKey() {
+	public IChromosomeType getSpeciesChromosomeType() {
 		return EnumTreeChromosome.SPECIES;
 	}
 

src/main/java/forestry/arboriculture/genetics/WoodProvider.java

@@ -13,12 +13,6 @@ package forestry.arboriculture.genetics;
 import javax.annotation.Nonnull;
 import java.util.Locale;
 
-import net.minecraft.client.renderer.texture.TextureAtlasSprite;
-import net.minecraft.client.renderer.texture.TextureMap;
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-import net.minecraft.util.ResourceLocation;
-
 import forestry.api.arboriculture.EnumForestryWoodType;
 import forestry.api.arboriculture.IWoodProvider;
 import forestry.api.arboriculture.TreeManager;
@@ -26,6 +20,11 @@ import forestry.api.arboriculture.WoodBlockKind;
 import forestry.api.core.ITextureManager;
 import forestry.core.config.Constants;
 import forestry.core.proxy.Proxies;
+import net.minecraft.client.renderer.texture.TextureAtlasSprite;
+import net.minecraft.client.renderer.texture.TextureMap;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.util.ResourceLocation;
 
 public class WoodProvider implements IWoodProvider {
 
@@ -61,4 +60,14 @@ public class WoodProvider implements IWoodProvider {
 		return TreeManager.woodAccess.getStack(woodType, WoodBlockKind.LOG, false);
 	}
 
+	@Override
+	public int getCombustibility() {
+		return woodType.getCombustability();
+	}
+
+	@Override
+	public int getCarbonization() {
+		return woodType.getCarbonization();
+	}
+
 }

src/main/java/forestry/arboriculture/genetics/WoodProviderVanilla.java

@@ -12,18 +12,17 @@ package forestry.arboriculture.genetics;
 
 import javax.annotation.Nonnull;
 
-import net.minecraft.client.renderer.texture.TextureAtlasSprite;
-import net.minecraft.client.renderer.texture.TextureMap;
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-import net.minecraft.util.ResourceLocation;
-
 import forestry.api.arboriculture.EnumVanillaWoodType;
 import forestry.api.arboriculture.IWoodProvider;
 import forestry.api.arboriculture.TreeManager;
 import forestry.api.arboriculture.WoodBlockKind;
 import forestry.api.core.ITextureManager;
 import forestry.core.proxy.Proxies;
+import net.minecraft.client.renderer.texture.TextureAtlasSprite;
+import net.minecraft.client.renderer.texture.TextureMap;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.util.ResourceLocation;
 
 public class WoodProviderVanilla implements IWoodProvider {
 
@@ -80,5 +79,15 @@ public class WoodProviderVanilla implements IWoodProvider {
 	public ItemStack getWoodStack() {
 		return TreeManager.woodAccess.getStack(woodType, WoodBlockKind.LOG, false);
 	}
-	
+
+	@Override
+	public int getCombustibility() {
+		return woodType.getCombustability();
+	}
+
+	@Override
+	public int getCarbonization() {
+		return woodType.getCarbonization();
+	}
+
 }

src/main/java/forestry/arboriculture/genetics/alleles/AlleleGrowth.java

@@ -18,10 +18,13 @@ import forestry.api.arboriculture.IAlleleGrowth;
 import forestry.api.arboriculture.IGrowthProvider;
 import forestry.api.genetics.AlleleManager;
 import forestry.arboriculture.genetics.GrowthProvider;
-import forestry.arboriculture.genetics.GrowthProviderTropical;
 import forestry.core.config.Constants;
 import forestry.core.genetics.alleles.AlleleCategorized;
 
+/**
+ * @deprecated this is being removed to simplify trees
+ */
+@Deprecated
 public class AlleleGrowth extends AlleleCategorized implements IAlleleGrowth {
 
 	public static IAlleleGrowth growthLightLevel;
@@ -32,7 +35,7 @@ public class AlleleGrowth extends AlleleCategorized implements IAlleleGrowth {
 		List<IAlleleGrowth> growthAlleles = Arrays.asList(
 				growthLightLevel = new AlleleGrowth("lightlevel", new GrowthProvider()),
 				growthAcacia = new AlleleGrowth("acacia", new GrowthProvider()),
-				growthTropical = new AlleleGrowth("tropical", new GrowthProviderTropical())
+				growthTropical = new AlleleGrowth("tropical", new GrowthProvider())
 		);
 
 		for (IAlleleGrowth alleleGrowth : growthAlleles) {

src/main/java/forestry/arboriculture/genetics/pollination/CheckPollinatableTree.java

@@ -10,12 +10,9 @@
  ******************************************************************************/
 package forestry.arboriculture.genetics.pollination;
 
-import java.util.EnumSet;
-
-import net.minecraftforge.common.EnumPlantType;
-
 import forestry.api.arboriculture.ITree;
 import forestry.api.genetics.ICheckPollinatable;
+import net.minecraftforge.common.EnumPlantType;
 
 public class CheckPollinatableTree implements ICheckPollinatable {
 
@@ -26,8 +23,8 @@ public class CheckPollinatableTree implements ICheckPollinatable {
 	}
 
 	@Override
-	public EnumSet<EnumPlantType> getPlantType() {
-		return tree.getPlantTypes();
+	public EnumPlantType getPlantType() {
+		return tree.getGenome().getPrimary().getPlantType();
 	}
 
 	@Override
@@ -40,9 +37,6 @@ public class CheckPollinatableTree implements ICheckPollinatable {
 		if (tree.getMate() != null) {
 			return false;
 		}
-		if (!(pollen instanceof ITree)) {
-			return false;
-		}
 
 		return !tree.isGeneticEqual(pollen);
 	}

src/main/java/forestry/arboriculture/items/ItemBlockPile.java

@@ -10,6 +10,14 @@
  ******************************************************************************/
 package forestry.arboriculture.items;
 
+import forestry.api.arboriculture.EnumPileType;
+import forestry.api.arboriculture.IAlleleTreeSpecies;
+import forestry.arboriculture.PluginArboriculture;
+import forestry.arboriculture.blocks.BlockPile;
+import forestry.arboriculture.tiles.TilePile;
+import forestry.core.items.ItemBlockForestry;
+import forestry.core.tiles.TileUtil;
+import forestry.core.utils.Translator;
 import net.minecraft.block.Block;
 import net.minecraft.block.state.IBlockState;
 import net.minecraft.entity.player.EntityPlayer;
@@ -17,15 +25,6 @@ import net.minecraft.item.ItemStack;
 import net.minecraft.util.EnumFacing;
 import net.minecraft.util.math.BlockPos;
 import net.minecraft.world.World;
-import forestry.api.arboriculture.EnumPileType;
-import forestry.api.arboriculture.ITree;
-import forestry.api.genetics.IAlleleSpecies;
-import forestry.arboriculture.PluginArboriculture;
-import forestry.arboriculture.blocks.BlockPile;
-import forestry.arboriculture.tiles.TilePile;
-import forestry.core.items.ItemBlockForestry;
-import forestry.core.tiles.TileUtil;
-import forestry.core.utils.Translator;
 
 public class ItemBlockPile<B extends Block> extends ItemBlockForestry<Block> {
 
@@ -52,12 +51,11 @@ public class ItemBlockPile<B extends Block> extends ItemBlockForestry<Block> {
 			if (!itemstack.hasTagCompound()) {
 				return "Unknown";
 			}
-			ITree tree = BlockPile.getTree(itemstack);
-			if (tree == null) {
+			IAlleleTreeSpecies species = BlockPile.getTreeSpecies(itemstack);
+			if (species == null) {
 				return "Unknown";
 			}
-			IAlleleSpecies species = tree.getGenome().getPrimary();
-	
+
 			String customTreeKey = "for.trees.custom.pile." + species.getUnlocalizedName().replace("trees.species.", "");
 			if (Translator.canTranslateToLocal(customTreeKey)) {
 				return Translator.translateToLocal(customTreeKey);

src/main/java/forestry/arboriculture/items/ItemGrafter.java

@@ -10,6 +10,9 @@
  ******************************************************************************/
 package forestry.arboriculture.items;
 
+import java.util.List;
+
+import forestry.core.utils.Translator;
 import net.minecraft.block.Block;
 import net.minecraft.block.BlockLeaves;
 import net.minecraft.block.material.Material;
@@ -34,6 +37,14 @@ public class ItemGrafter extends ItemForestryTool implements IToolGrafter {
 		setEfficiencyOnProperMaterial(4.0f);
 	}
 
+	@Override
+	public void addInformation(ItemStack stack, EntityPlayer playerIn, List<String> tooltip, boolean advanced) {
+		super.addInformation(stack, playerIn, tooltip, advanced);
+		if (!stack.isItemDamaged()) {
+			tooltip.add(Translator.translateToLocalFormatted("item.for.uses", stack.getMaxDamage() + 1));
+		}
+	}
+
 	@Override
 	public boolean canHarvestBlock(IBlockState state, ItemStack stack) {
 		Block block = state.getBlock();

src/main/java/forestry/arboriculture/items/ItemRegistryArboriculture.java

@@ -10,6 +10,8 @@
  ******************************************************************************/
 package forestry.arboriculture.items;
 
+import net.minecraft.init.Items;
+import net.minecraft.item.ItemStack;
 import net.minecraftforge.oredict.OreDictionary;
 
 import forestry.api.arboriculture.EnumGermlingType;
@@ -28,8 +30,12 @@ public class ItemRegistryArboriculture extends ItemRegistry {
 		OreDictionary.registerOre(OreDictUtil.TREE_SAPLING, sapling.getWildcard());
 		
 		pollenFertile = registerItem(new ItemGermlingGE(EnumGermlingType.POLLEN), "pollenFertile");
+
 		charcoal = registerItem(new ItemCharcoal(), "charcoal");
-		grafter = registerItem(new ItemGrafter(4), "grafter");
+		registerOreDict(OreDictUtil.CHARCOAL, new ItemStack(charcoal, 1, OreDictionary.WILDCARD_VALUE));
+		registerOreDict(OreDictUtil.CHARCOAL, new ItemStack(Items.COAL, 1, 1));
+
+		grafter = registerItem(new ItemGrafter(9), "grafter");
 		grafterProven = registerItem(new ItemGrafter(149), "grafterProven");
 	}
 }

src/main/java/forestry/arboriculture/models/ModelWoodPile.java

@@ -7,11 +7,9 @@ import java.util.Map;
 
 import com.google.common.base.Function;
 import com.google.common.collect.ImmutableMap;
-
 import forestry.api.arboriculture.IAlleleTreeSpecies;
-import forestry.api.arboriculture.ITree;
 import forestry.api.arboriculture.TreeManager;
-import forestry.arboriculture.genetics.Tree;
+import forestry.arboriculture.blocks.BlockPile;
 import forestry.arboriculture.genetics.TreeDefinition;
 import forestry.arboriculture.tiles.TilePile;
 import forestry.core.blocks.propertys.UnlistedBlockAccess;
@@ -62,9 +60,9 @@ public class ModelWoodPile extends BlankItemModel{
 			if(pile == null){
 				return Collections.emptyList();
 			}
-			ITree tree = pile.getTree();
-			if (tree == null) {
-				tree = TreeManager.treeRoot.templateAsIndividual(TreeManager.treeRoot.getDefaultTemplate());
+			IAlleleTreeSpecies treeSpecies = pile.getTreeSpecies();
+			if (treeSpecies == null) {
+				treeSpecies = (IAlleleTreeSpecies) TreeManager.treeRoot.getDefaultTemplate()[TreeManager.treeRoot.getSpeciesChromosomeType().ordinal()];
 			}
 			
 			if (modelWoodPileBlock == null) {
@@ -77,8 +75,8 @@ public class ModelWoodPile extends BlankItemModel{
 					return Collections.emptyList();
 				}
 			}
-			
-			IBakedModel model = bakeModel(tree, false);
+
+			IBakedModel model = bakeModel(treeSpecies, false);
 			return model.getQuads(state, side, rand);
 		}
 		return Collections.emptyList();
@@ -103,10 +101,9 @@ public class ModelWoodPile extends BlankItemModel{
 	protected ItemOverrideList createOverrides() {
 		return new PileItemOverrideList();
 	}
-	
-	private IBakedModel bakeModel(ITree tree, boolean isItem) {
+
+	private IBakedModel bakeModel(IAlleleTreeSpecies treeSpecies, boolean isItem) {
 		ImmutableMap.Builder<String, String> textures = ImmutableMap.builder();
-		IAlleleTreeSpecies treeSpecies = tree.getGenome().getPrimary();
 		String treeUID = treeSpecies.getUID();
 		Map<String, IBakedModel> map = isItem ? itemCache : blockCache;
 		if(!map.containsKey(treeUID)){
@@ -135,14 +132,11 @@ public class ModelWoodPile extends BlankItemModel{
 					return null;
 				}
 			}
-			ITree tree = null;
-			if(stack.hasTagCompound()){
-				tree = new Tree(stack.getTagCompound().getCompoundTag("ContainedTree"));
+			IAlleleTreeSpecies treeSpecies = BlockPile.getTreeSpecies(stack);
+			if (treeSpecies == null) {
+				treeSpecies = (IAlleleTreeSpecies) TreeManager.treeRoot.getDefaultTemplate()[TreeManager.treeRoot.getSpeciesChromosomeType().ordinal()];
 			}
-			if (tree == null) {
-				tree = TreeManager.treeRoot.templateAsIndividual(TreeManager.treeRoot.getDefaultTemplate());
-			}
-			return bakeModel(tree, true);
+			return bakeModel(treeSpecies, true);
 		}
 	}
 

src/main/java/forestry/arboriculture/multiblock/CharcoalPileController.java

@@ -4,13 +4,8 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.tileentity.TileEntity;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
 import forestry.api.arboriculture.EnumPileType;
+import forestry.api.arboriculture.IWoodProvider;
 import forestry.api.core.EnumHumidity;
 import forestry.api.core.EnumTemperature;
 import forestry.api.multiblock.ICharcoalPileComponent;
@@ -28,6 +23,11 @@ import forestry.core.network.DataOutputStreamForestry;
 import forestry.core.proxy.Proxies;
 import forestry.core.utils.Log;
 import forestry.core.utils.Translator;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.tileentity.TileEntity;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
 
 public class CharcoalPileController extends RectangularMultiblockControllerBase implements ICharcoalPileControllerInternal {
 
@@ -115,11 +115,12 @@ public class CharcoalPileController extends RectangularMultiblockControllerBase
 		if(woodBurnTime == 0){
 			int comps = 0;
 			int newBurnTime = 0;
-			for(IMultiblockComponent part : connectedParts){
+			for (IMultiblockComponent part : connectedParts) {
 				ICharcoalPileComponent comp = (ICharcoalPileComponent) part;
-				if(comp.getTree() != null){
+				if (comp.getTreeSpecies() != null) {
 					comps++;
-					newBurnTime+= comp.getTree().getGenome().getCombustibility() * 1000;
+					IWoodProvider woodProvider = comp.getTreeSpecies().getWoodProvider();
+					newBurnTime += woodProvider.getCombustibility() * 1000;
 				}
 			}
 			woodBurnTime = newBurnTime / comps;

src/main/java/forestry/arboriculture/render/CharcoalPileRenderer.java

@@ -12,18 +12,10 @@ package forestry.arboriculture.render;
 
 import javax.annotation.Nonnull;
 
-import static forestry.arboriculture.multiblock.EnumPilePosition.BACK;
-import static forestry.arboriculture.multiblock.EnumPilePosition.CORNER_BACK_LEFT;
-import static forestry.arboriculture.multiblock.EnumPilePosition.CORNER_BACK_RIGHT;
-import static forestry.arboriculture.multiblock.EnumPilePosition.FRONT;
-import static forestry.arboriculture.multiblock.EnumPilePosition.CORNER_FRONT_LEFT;
-import static forestry.arboriculture.multiblock.EnumPilePosition.CORNER_FRONT_RIGHT;
-import static forestry.arboriculture.multiblock.EnumPilePosition.SIDE_LEFT;
-import static forestry.arboriculture.multiblock.EnumPilePosition.SIDE_RIGHT;
+import static forestry.arboriculture.multiblock.EnumPilePosition.*;
 
 import forestry.api.arboriculture.EnumPileType;
 import forestry.api.arboriculture.IAlleleTreeSpecies;
-import forestry.api.arboriculture.ITree;
 import forestry.api.arboriculture.TreeManager;
 import forestry.arboriculture.blocks.BlockPile;
 import forestry.arboriculture.multiblock.EnumPilePosition;
@@ -67,11 +59,10 @@ public class CharcoalPileRenderer extends TileEntitySpecialRenderer<TilePile> {
 			boolean isOnTop = logic.getController().getMaximumCoord().getY() == pile.getPos().getY();
 			// TODO Add brightness to the textures.
 			int brightness = state.getPackedLightmapCoords(pile.getWorld(), pile.getPos());
-			ITree tree = pile.getNextWoodPile();
-			if (tree == null) {
-				tree = TreeManager.treeRoot.templateAsIndividual(TreeManager.treeRoot.getDefaultTemplate());
+			IAlleleTreeSpecies treeSpecies = pile.getNextWoodPile();
+			if (treeSpecies == null) {
+				treeSpecies = (IAlleleTreeSpecies) TreeManager.treeRoot.getDefaultTemplate()[TreeManager.treeRoot.getSpeciesChromosomeType().ordinal()];
 			}
-			IAlleleTreeSpecies treeSpecies = tree.getGenome().getPrimary();
 			TextureAtlasSprite dirtSprite;
 			if(pile.getPileType() == EnumPileType.ASH){
 				dirtSprite = TextureManager.registerSprite(new ResourceLocation("forestry:blocks/ash"));

src/main/java/forestry/arboriculture/render/PileParticleCallback.java

@@ -1,18 +1,17 @@
 package forestry.arboriculture.render;
 
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.client.particle.ParticleDigging;
-import net.minecraft.client.renderer.texture.TextureAtlasSprite;
-import net.minecraft.util.ResourceLocation;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
 import forestry.api.arboriculture.EnumPileType;
 import forestry.arboriculture.blocks.BlockPile;
 import forestry.arboriculture.tiles.TilePile;
 import forestry.core.render.ParticleHelper;
 import forestry.core.render.TextureManager;
 import forestry.core.tiles.TileUtil;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.client.particle.ParticleDigging;
+import net.minecraft.client.renderer.texture.TextureAtlasSprite;
+import net.minecraft.util.ResourceLocation;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
 
 public class PileParticleCallback extends ParticleHelper.DefaultCallback<BlockPile>{
 
@@ -25,14 +24,14 @@ public class PileParticleCallback extends ParticleHelper.DefaultCallback<BlockPi
 		EnumPileType type = block.getPileType();
 		TilePile pile = TileUtil.getTile(world, pos, TilePile.class);
 		TextureAtlasSprite texture;
-		if(type == EnumPileType.DIRT){
+		if (type == EnumPileType.DIRT) {
 			texture = TextureManager.registerSprite(new ResourceLocation("forestry:blocks/loam"));
-		}else if(type == EnumPileType.WOOD){
-			if(pile == null || pile.getTree() == null){
+		} else if (type == EnumPileType.WOOD) {
+			if (pile == null || pile.getTreeSpecies() == null) {
 				super.setTexture(fx, world, pos, state);
 				return;
 			}
-			texture = pile.getTree().getGenome().getPrimary().getWoodProvider().getSprite(false);
+			texture = pile.getTreeSpecies().getWoodProvider().getSprite(false);
 		}else{
 			texture = TextureManager.registerSprite(new ResourceLocation("forestry:blocks/ash"));
 		}

src/main/java/forestry/arboriculture/tiles/TileLeaves.java

@@ -15,20 +15,9 @@ import javax.annotation.Nullable;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.EnumSet;
 import java.util.List;
 import java.util.Random;
 
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.entity.player.EntityPlayer;
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.util.ResourceLocation;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
-import net.minecraftforge.common.EnumPlantType;
-
 import forestry.api.arboriculture.EnumTreeChromosome;
 import forestry.api.arboriculture.IAlleleTreeSpecies;
 import forestry.api.arboriculture.IFruitProvider;
@@ -59,6 +48,14 @@ import forestry.core.network.packets.PacketTileStream;
 import forestry.core.proxy.Proxies;
 import forestry.core.utils.ColourUtil;
 import forestry.core.utils.GeneticsUtil;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.entity.player.EntityPlayer;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.util.ResourceLocation;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
+import net.minecraftforge.common.EnumPlantType;
 
 public class TileLeaves extends TileTreeContainer implements IPollinatable, IFruitBearer, IButterflyNursery, IRipeningPacketReceiver {
 
@@ -258,13 +255,13 @@ public class TileLeaves extends TileTreeContainer implements IPollinatable, IFru
 
 	/* IPOLLINATABLE */
 	@Override
-	public EnumSet<EnumPlantType> getPlantType() {
+	public EnumPlantType getPlantType() {
 		ITree tree = getTree();
 		if (tree == null) {
-			return EnumSet.noneOf(EnumPlantType.class);
+			return EnumPlantType.Plains;
 		}
 
-		return tree.getPlantTypes();
+		return tree.getGenome().getPrimary().getPlantType();
 	}
 
 	@Override

src/main/java/forestry/arboriculture/tiles/TilePile.java

@@ -2,20 +2,9 @@ package forestry.arboriculture.tiles;
 
 import javax.annotation.Nonnull;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.entity.player.EntityPlayer;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
-import net.minecraftforge.fml.relauncher.Side;
-import net.minecraftforge.fml.relauncher.SideOnly;
-
 import forestry.api.arboriculture.EnumPileType;
-import forestry.api.arboriculture.ITree;
-import forestry.api.arboriculture.TreeManager;
-import forestry.api.genetics.IAllele;
+import forestry.api.arboriculture.IAlleleTreeSpecies;
+import forestry.api.genetics.AlleleManager;
 import forestry.api.multiblock.ICharcoalPileComponent;
 import forestry.api.multiblock.IMultiblockController;
 import forestry.arboriculture.PluginArboriculture;
@@ -25,11 +14,18 @@ import forestry.arboriculture.multiblock.EnumPilePosition;
 import forestry.arboriculture.multiblock.MultiblockLogicCharcoalPile;
 import forestry.core.multiblock.MultiblockTileEntityForestry;
 import forestry.core.tiles.TileUtil;
+import net.minecraft.block.Block;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.entity.player.EntityPlayer;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
+import net.minecraftforge.fml.relauncher.Side;
+import net.minecraftforge.fml.relauncher.SideOnly;
 
 public class TilePile extends MultiblockTileEntityForestry<MultiblockLogicCharcoalPile> implements ICharcoalPileComponent<MultiblockLogicCharcoalPile>{
 
-	@Nonnull
-	private ITree containedTree;
+	private IAlleleTreeSpecies treeSpecies;
 	@SideOnly(Side.CLIENT)
 	private BlockPos woodPos;
 
@@ -53,7 +49,7 @@ public class TilePile extends MultiblockTileEntityForestry<MultiblockLogicCharco
 	@Override
 	public boolean shouldRefresh(World world, BlockPos pos, IBlockState oldState, IBlockState newState) {
 		Block newBlock = newState.getBlock();
-		return oldState.getBlock() != newState.getBlock() && newState.getBlock() != PluginArboriculture.blocks.piles.get(EnumPileType.ASH);
+		return oldState.getBlock() != newBlock && newBlock != PluginArboriculture.blocks.piles.get(EnumPileType.ASH);
 	}
 
 	@Override
@@ -131,20 +127,20 @@ public class TilePile extends MultiblockTileEntityForestry<MultiblockLogicCharco
 		return getBlockType().getDefaultState().withProperty(BlockPile.PILE_POSITION, pileType);
 	}
 	
-	private static ITree getTree(String speciesUID) {
-		IAllele[] treeTemplate = TreeManager.treeRoot.getTemplate(speciesUID);
-		if (treeTemplate == null) {
-			return null;
-		}
-		return TreeManager.treeRoot.templateAsIndividual(treeTemplate);
-	}
-	
 	@Override
 	public void readFromNBT(NBTTagCompound data) {
 		super.readFromNBT(data);
-		
+
+		// legacy
 		if (data.hasKey("ContainedTree")) {
-			setTree(new Tree(data.getCompoundTag("ContainedTree")));
+			Tree containedTree = new Tree(data.getCompoundTag("ContainedTree"));
+			setTreeSpecies(containedTree.getGenome().getPrimary());
+		}
+
+		if (data.hasKey("TreeSpecies")) {
+			String treeSpeciesUid = data.getString("TreeSpecies");
+			IAlleleTreeSpecies treeSpecies = (IAlleleTreeSpecies) AlleleManager.alleleRegistry.getAllele(treeSpeciesUid);
+			setTreeSpecies(treeSpecies);
 		}
 	}
 	
@@ -152,11 +148,8 @@ public class TilePile extends MultiblockTileEntityForestry<MultiblockLogicCharco
 	@Override
 	public NBTTagCompound writeToNBT(NBTTagCompound data) {
 		data = super.writeToNBT(data);
-		
-		if (containedTree != null) {
-			NBTTagCompound subcompound = new NBTTagCompound();
-			containedTree.writeToNBT(subcompound);
-			data.setTag("ContainedTree", subcompound);
+		if (treeSpecies != null) {
+			data.setString("TreeSpecies", treeSpecies.getUID());
 		}
 		return data;
 	}
@@ -164,18 +157,18 @@ public class TilePile extends MultiblockTileEntityForestry<MultiblockLogicCharco
 	@Override
 	protected void encodeDescriptionPacket(NBTTagCompound packetData) {
 		super.encodeDescriptionPacket(packetData);
-		if (containedTree != null) {
-			NBTTagCompound subcompound = new NBTTagCompound();
-			containedTree.writeToNBT(subcompound);
-			packetData.setTag("ContainedTree", subcompound);
+		if (treeSpecies != null) {
+			packetData.setString("TreeSpecies", treeSpecies.getUID());
 		}
 	}
 
 	@Override
 	protected void decodeDescriptionPacket(NBTTagCompound packetData) {
 		super.decodeDescriptionPacket(packetData);
-		if (packetData.hasKey("ContainedTree")) {
-			setTree(new Tree(packetData.getCompoundTag("ContainedTree")));
+		if (packetData.hasKey("TreeSpecies")) {
+			String treeSpeciesUid = packetData.getString("TreeSpecies");
+			IAlleleTreeSpecies treeSpecies = (IAlleleTreeSpecies) AlleleManager.alleleRegistry.getAllele(treeSpeciesUid);
+			setTreeSpecies(treeSpecies);
 		}
 	}
 	
@@ -183,17 +176,16 @@ public class TilePile extends MultiblockTileEntityForestry<MultiblockLogicCharco
 	
 	/* CONTAINED TREE */
 	@Override
-	public void setTree(@Nonnull ITree tree) {
-		this.containedTree = tree;
+	public void setTreeSpecies(@Nonnull IAlleleTreeSpecies treeSpecies) {
+		this.treeSpecies = treeSpecies;
 		if (worldObj != null && worldObj.isRemote) {
 			worldObj.markBlockRangeForRenderUpdate(getPos(), getPos());
 		}
 	}
 	
 	@Override
-	@Nonnull
-	public ITree getTree() {
-		return this.containedTree;
+	public IAlleleTreeSpecies getTreeSpecies() {
+		return this.treeSpecies;
 	}
 	
 	@Override
@@ -204,13 +196,13 @@ public class TilePile extends MultiblockTileEntityForestry<MultiblockLogicCharco
 	
 	@Override
 	@SideOnly(Side.CLIENT)
-	public ITree getNextWoodPile(){
+	public IAlleleTreeSpecies getNextWoodPile() {
 		if(woodPos == null){
 			woodPos = getNextWoodPilePos();
 		}
 		TilePile pile = TileUtil.getTile(worldObj, woodPos, TilePile.class);
-		if(pile != null){
-			return pile.getTree();
+		if (pile != null) {
+			return pile.getTreeSpecies();
 		}
 		return null;
 	}

src/main/java/forestry/arboriculture/worldgen/WorldGenBalsa.java

@@ -10,18 +10,14 @@
  ******************************************************************************/
 package forestry.arboriculture.worldgen;
 
-import javax.annotation.Nonnull;
-import java.util.Collections;
 import java.util.List;
 import java.util.Random;
-import java.util.Set;
-
-import net.minecraft.util.EnumFacing;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
 
 import forestry.api.world.ITreeGenData;
 import forestry.core.worldgen.WorldGenHelper;
+import net.minecraft.util.EnumFacing;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
 
 public class WorldGenBalsa extends WorldGenTree {
 
@@ -31,7 +27,8 @@ public class WorldGenBalsa extends WorldGenTree {
 
 	@Override
 	protected void generateLeaves(World world, Random rand, TreeBlockTypeLeaf leaf, List<BlockPos> branchEnds, BlockPos startPos) {
-		BlockPos.MutableBlockPos leafCenter = new BlockPos.MutableBlockPos(startPos.add(0, height, 0));
+		BlockPos topPos = startPos.add(0, height + 1, 0);
+		BlockPos.MutableBlockPos leafCenter = new BlockPos.MutableBlockPos(topPos);
 		float leafRadius = (girth - 1.0f) / 2.0f;
 
 		WorldGenHelper.addBlock(world, leafCenter, leaf, WorldGenHelper.EnumReplaceMode.AIR);
@@ -44,7 +41,7 @@ public class WorldGenBalsa extends WorldGenTree {
 			leafCenter.move(EnumFacing.DOWN);
 		}
 
-		while (leafCenter.getY() > 6) {
+		while (leafCenter.getY() > topPos.getY() - 6) {
 			WorldGenHelper.generateCylinderFromPos(world, leaf, leafCenter, leafRadius + girth, 1, WorldGenHelper.EnumReplaceMode.SOFT);
 			leafCenter.move(EnumFacing.DOWN);
 		}

src/main/java/forestry/core/config/Config.java

@@ -10,8 +10,6 @@
  ******************************************************************************/
 package forestry.core.config;
 
-import com.google.common.collect.LinkedListMultimap;
-
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -24,13 +22,13 @@ import java.util.HashSet;
 import java.util.Properties;
 import java.util.Set;
 
-import net.minecraftforge.common.config.Property;
-
+import com.google.common.collect.LinkedListMultimap;
 import forestry.Forestry;
 import forestry.core.fluids.Fluids;
 import forestry.core.utils.Log;
 import forestry.core.utils.Translator;
 import forestry.mail.gui.GuiMailboxInfo;
+import net.minecraftforge.common.config.Property;
 
 public class Config {
 
@@ -54,7 +52,6 @@ public class Config {
 	public static boolean enableParticleFX = true;
 
 	// Genetics
-	public static boolean clearInvalidChromosomes = false;
 	public static boolean pollinateVanillaTrees = true;
 	public static float researchMutationBoostMultiplier = 1.5f;
 	public static float maxResearchMutationBoostPercent = 5.0f;
@@ -204,7 +201,6 @@ public class Config {
 			collectorStamps.addAll(Arrays.asList(defaultCollectors));
 		}
 
-		clearInvalidChromosomes = configCommon.getBooleanLocalized("genetics", "clear.invalid.chromosomes", clearInvalidChromosomes);
 		pollinateVanillaTrees = configCommon.getBooleanLocalized("genetics", "pollinate.vanilla.trees", pollinateVanillaTrees);
 		researchMutationBoostMultiplier = configCommon.getFloatLocalized("genetics.research.boost", "multiplier", researchMutationBoostMultiplier, 1.0f, 1000.f);
 		maxResearchMutationBoostPercent = configCommon.getFloatLocalized("genetics.research.boost", "max.percent", maxResearchMutationBoostPercent, 0.0f, 100.0f);

src/main/java/forestry/core/genetics/Chromosome.java

@@ -11,14 +11,15 @@
 package forestry.core.genetics;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.util.Random;
 
-import net.minecraft.nbt.NBTTagCompound;
-
 import forestry.api.genetics.AlleleManager;
 import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IChromosome;
-import forestry.core.utils.Log;
+import forestry.api.genetics.IChromosomeType;
+import forestry.api.genetics.ISpeciesRoot;
+import net.minecraft.nbt.NBTTagCompound;
 
 public class Chromosome implements IChromosome {
 
@@ -30,7 +31,37 @@ public class Chromosome implements IChromosome {
 	@Nonnull
 	private final IAllele secondary;
 
-	// / CONSTRUCTOR
+	@Nonnull
+	public static Chromosome create(@Nullable String primarySpeciesUid, @Nullable String secondarySpeciesUid, @Nonnull IChromosomeType chromosomeType, @Nonnull NBTTagCompound nbt) {
+		IAllele primary = AlleleManager.alleleRegistry.getAllele(nbt.getString(UID0_TAG));
+		IAllele secondary = AlleleManager.alleleRegistry.getAllele(nbt.getString(UID1_TAG));
+
+		primary = validateAllele(primarySpeciesUid, chromosomeType, primary);
+		secondary = validateAllele(secondarySpeciesUid, chromosomeType, secondary);
+
+		return new Chromosome(primary, secondary);
+	}
+
+	@Nonnull
+	private static IAllele validateAllele(@Nullable String speciesUid, @Nonnull IChromosomeType chromosomeType, @Nullable IAllele allele) {
+		if (!chromosomeType.getAlleleClass().isInstance(allele)) {
+			ISpeciesRoot speciesRoot = chromosomeType.getSpeciesRoot();
+
+			IAllele[] template = null;
+
+			if (speciesUid != null) {
+				template = speciesRoot.getTemplate(speciesUid);
+			}
+
+			if (template == null) {
+				template = speciesRoot.getDefaultTemplate();
+			}
+
+			return template[chromosomeType.ordinal()];
+		}
+		return allele;
+	}
+
 	public Chromosome(@Nonnull IAllele allele) {
 		primary = secondary = allele;
 	}
@@ -40,11 +71,6 @@ public class Chromosome implements IChromosome {
 		this.secondary = secondary;
 	}
 
-	public Chromosome(@Nonnull NBTTagCompound nbt) {
-		primary = AlleleManager.alleleRegistry.getAllele(nbt.getString(UID0_TAG));
-		secondary = AlleleManager.alleleRegistry.getAllele(nbt.getString(UID1_TAG));
-	}
-
 	@Override
 	public NBTTagCompound writeToNBT(NBTTagCompound nbttagcompound) {
 		nbttagcompound.setString(UID0_TAG, primary.getUID());
@@ -64,9 +90,6 @@ public class Chromosome implements IChromosome {
 
 	@Override
 	public IAllele getActiveAllele() {
-		if (primary == null || secondary == null) {
-			return null;
-		}
 		if (primary.isDominant()) {
 			return primary;
 		}
@@ -89,38 +112,6 @@ public class Chromosome implements IChromosome {
 		return secondary;
 	}
 
-	public IAllele getRandomAllele(Random rand) {
-		if (rand.nextBoolean()) {
-			return primary;
-		} else {
-			return secondary;
-		}
-	}
-	
-	public boolean hasInvalidAlleles(Class<? extends IAllele> chromosomeClass) {
-		if (primary == null) {
-			Log.warning("Missing primary allele: {}", this);
-			return true;
-		}
-
-		if (!chromosomeClass.isInstance(primary)) {
-			Log.warning("Wrong primary allele for: {}. Should be: {}", this, chromosomeClass.getSimpleName());
-			return true;
-		}
-		
-		if (secondary == null) {
-			Log.warning("Missing secondary allele: {}", this);
-			return true;
-		}
-
-		if (!chromosomeClass.isInstance(secondary)) {
-			Log.warning("Wrong secondary allele for: {}. Should be: {}", this, chromosomeClass.getSimpleName());
-			return true;
-		}
-		
-		return false;
-	}
-
 	/* HELPER FUNCTIONS */
 	public static IChromosome inheritChromosome(Random rand, IChromosome parent1, IChromosome parent2) {
 

src/main/java/forestry/core/genetics/Genome.java

@@ -10,23 +10,20 @@
  ******************************************************************************/
 package forestry.core.genetics;
 
-import com.google.common.base.Objects;
-
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.util.Arrays;
 
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.nbt.NBTTagList;
-
+import com.google.common.base.Objects;
 import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IChromosome;
 import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IGenome;
 import forestry.api.genetics.ISpeciesRoot;
-import forestry.core.config.Config;
-import forestry.core.utils.Log;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.nbt.NBTTagList;
 
 public abstract class Genome implements IGenome {
 
@@ -115,15 +112,12 @@ public abstract class Genome implements IGenome {
 	 * Quickly gets the species without loading the whole genome.
 	 * We need this because the client uses the species for rendering.
 	 */
-	public static IAlleleSpecies getSpeciesDirectly(ItemStack itemStack) {
+	@Nullable
+	public static IAlleleSpecies getSpeciesDirectly(@Nonnull ISpeciesRoot speciesRoot, @Nonnull ItemStack itemStack) {
 		NBTTagCompound nbtTagCompound = itemStack.getTagCompound();
 		if (nbtTagCompound == null) {
 			return null;
 		}
-		return getSpeciesDirectly(nbtTagCompound);
-	}
-
-	public static IAlleleSpecies getSpeciesDirectly(@Nonnull NBTTagCompound nbtTagCompound) {
 
 		NBTTagCompound genomeNBT = nbtTagCompound.getCompoundTag("Genome");
 		if (genomeNBT == null) {
@@ -136,7 +130,7 @@ public abstract class Genome implements IGenome {
 		}
 
 		NBTTagCompound chromosomeNBT = chromosomesNBT.getCompoundTagAt(0);
-		Chromosome chromosome = new Chromosome(chromosomeNBT);
+		Chromosome chromosome = Chromosome.create(null, null, speciesRoot.getSpeciesChromosomeType(), chromosomeNBT);
 
 		IAllele activeAllele = chromosome.getActiveAllele();
 		if (!(activeAllele instanceof IAlleleSpecies)) {
@@ -170,23 +164,21 @@ public abstract class Genome implements IGenome {
 		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) {
-				Chromosome chromosome = new Chromosome(chromosomeNBT);
+				IChromosomeType chromosomeType = speciesRoot.getKaryotype()[chromosomeOrdinal];
+				Chromosome chromosome = Chromosome.create(primarySpeciesUid, secondarySpeciesUid, chromosomeType, chromosomeNBT);
 				chromosomes[chromosomeOrdinal] = chromosome;
 
-				IChromosomeType chromosomeType = speciesRoot.getKaryotype()[chromosomeOrdinal];
-				if (chromosome.hasInvalidAlleles(chromosomeType.getAlleleClass())) {
-					if (Config.clearInvalidChromosomes) {
-						Log.warning("Found Chromosome with invalid Alleles. Config is set to clear invalid chromosomes, replacing with the default.");
-						IAllele[] defaultTemplate = speciesRoot.getDefaultTemplate();
-						return speciesRoot.templateAsChromosomes(defaultTemplate);
-					} else {
-						throw new RuntimeException("Found Chromosome with invalid Alleles.\nNBTTagCompound: " + chromosomesNBT + "\nSee config option \"genetics.clear.invalid.chromosomes\".\nMissing: " + chromosomeNBT);
-					}
+				if (chromosomeOrdinal == speciesRoot.getSpeciesChromosomeType().ordinal()) {
+					primarySpeciesUid = chromosome.getPrimaryAllele().getUID();
+					secondarySpeciesUid = chromosome.getSecondaryAllele().getUID();
 				}
 			}
 		}

src/main/java/forestry/core/genetics/ItemResearchNote.java

@@ -14,19 +14,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Locale;
 
-import net.minecraft.entity.player.EntityPlayer;
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.util.ActionResult;
-import net.minecraft.util.EnumActionResult;
-import net.minecraft.util.EnumHand;
-import net.minecraft.util.text.TextComponentTranslation;
-import net.minecraft.util.text.TextFormatting;
-import net.minecraft.world.World;
-
 import com.mojang.authlib.GameProfile;
-
 import forestry.api.genetics.AlleleManager;
 import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IAlleleSpecies;
@@ -38,6 +26,16 @@ import forestry.core.items.ItemForestry;
 import forestry.core.proxy.Proxies;
 import forestry.core.utils.PlayerUtil;
 import forestry.core.utils.Translator;
+import net.minecraft.entity.player.EntityPlayer;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.util.ActionResult;
+import net.minecraft.util.EnumActionResult;
+import net.minecraft.util.EnumHand;
+import net.minecraft.util.text.TextComponentTranslation;
+import net.minecraft.util.text.TextFormatting;
+import net.minecraft.world.World;
 
 public class ItemResearchNote extends ItemForestry {
 
@@ -94,7 +92,7 @@ public class ItemResearchNote extends ItemForestry {
 				String species2 = encoded.getAllele1().getName();
 				String mutationChanceKey = EnumMutateChance.rateChance(encoded.getBaseChance()).toString().toLowerCase(Locale.ENGLISH);
 				String mutationChance = Translator.translateToLocal("for.researchNote.chance." + mutationChanceKey);
-				String speciesResult = encoded.getTemplate()[root.getKaryotypeKey().ordinal()].getName();
+				String speciesResult = encoded.getTemplate()[root.getSpeciesChromosomeType().ordinal()].getName();
 
 				tooltips.add(Translator.translateToLocal("for.researchNote.discovery.0"));
 				tooltips.add(Translator.translateToLocal("for.researchNote.discovery.1").replace("%SPEC1", species1).replace("%SPEC2", species2));
@@ -147,7 +145,7 @@ public class ItemResearchNote extends ItemForestry {
 
 				IAlleleSpecies species0 = encoded.getAllele0();
 				IAlleleSpecies species1 = encoded.getAllele1();
-				IAlleleSpecies speciesResult = (IAlleleSpecies) encoded.getTemplate()[root.getKaryotypeKey().ordinal()];
+				IAlleleSpecies speciesResult = (IAlleleSpecies) encoded.getTemplate()[root.getSpeciesChromosomeType().ordinal()];
 
 				tracker.registerSpecies(species0);
 				tracker.registerSpecies(species1);

src/main/java/forestry/core/genetics/SpeciesRoot.java

@@ -20,14 +20,13 @@ import java.util.List;
 import java.util.Map;
 import java.util.Random;
 
-import net.minecraft.item.ItemStack;
-
 import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IChromosome;
 import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IMutation;
 import forestry.api.genetics.ISpeciesRoot;
+import net.minecraft.item.ItemStack;
 
 public abstract class SpeciesRoot implements ISpeciesRoot {
 	
@@ -82,8 +81,8 @@ public abstract class SpeciesRoot implements ISpeciesRoot {
 
 	/* MUTATIONS */
 	@Override
-	public Collection<? extends IMutation> getCombinations(IAllele other) {
-		ArrayList<IMutation> combinations = new ArrayList<>();
+	public List<IMutation> getCombinations(IAllele other) {
+		List<IMutation> combinations = new ArrayList<>();
 		for (IMutation mutation : getMutations(false)) {
 			if (mutation.isPartner(other)) {
 				combinations.add(mutation);

src/main/java/forestry/core/genetics/alleles/AlleleSpecies.java

@@ -11,20 +11,17 @@
 package forestry.core.genetics.alleles;
 
 import javax.annotation.Nonnull;
-import java.util.Collection;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Map;
 
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-import net.minecraft.world.World;
-
 import com.mojang.authlib.GameProfile;
-
 import forestry.api.core.EnumHumidity;
 import forestry.api.core.EnumTemperature;
 import forestry.api.genetics.AlleleManager;
 import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IAlleleSpeciesBuilder;
+import forestry.api.genetics.IBreedingTracker;
 import forestry.api.genetics.IClassification;
 import forestry.api.genetics.IIndividual;
 import forestry.api.genetics.IMutation;
@@ -33,6 +30,9 @@ import forestry.apiculture.items.ItemRegistryApiculture;
 import forestry.core.utils.GeneticsUtil;
 import forestry.core.utils.ItemStackUtil;
 import forestry.core.utils.Translator;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.world.World;
 
 public abstract class AlleleSpecies extends Allele implements IAlleleSpeciesBuilder, IAlleleSpecies {
 	private final String binomial;
@@ -103,7 +103,7 @@ public abstract class AlleleSpecies extends Allele implements IAlleleSpeciesBuil
 		if (complexityOverride != null) {
 			return complexityOverride;
 		}
-		return GeneticsUtil.getResearchComplexity(this, getRoot().getKaryotypeKey());
+		return GeneticsUtil.getResearchComplexity(this, getRoot().getSpeciesChromosomeType());
 	}
 
 	@Override
@@ -113,20 +113,30 @@ public abstract class AlleleSpecies extends Allele implements IAlleleSpeciesBuil
 
 	@Override
 	public ItemStack[] getResearchBounty(World world, GameProfile researcher, IIndividual individual, int bountyLevel) {
-		ItemStack research = null;
-		if (world.rand.nextFloat() < (float) 10 / bountyLevel) {
-			Collection<? extends IMutation> combinations = getRoot().getCombinations(this);
-			if (!combinations.isEmpty()) {
-				IMutation[] candidates = combinations.toArray(new IMutation[combinations.size()]);
-				research = AlleleManager.alleleRegistry.getMutationNoteStack(researcher, candidates[world.rand.nextInt(candidates.length)]);
+		if (world.rand.nextFloat() < bountyLevel / 32.0f) {
+			List<? extends IMutation> allMutations = getRoot().getCombinations(this);
+			if (!allMutations.isEmpty()) {
+				List<IMutation> unresearchedMutations = new ArrayList<>();
+				IBreedingTracker tracker = individual.getGenome().getSpeciesRoot().getBreedingTracker(world, researcher);
+				for (IMutation mutation : allMutations) {
+					if (!tracker.isResearched(mutation)) {
+						unresearchedMutations.add(mutation);
+					}
+				}
+
+				IMutation chosenMutation;
+				if (!unresearchedMutations.isEmpty()) {
+					chosenMutation = unresearchedMutations.get(world.rand.nextInt(unresearchedMutations.size()));
+				} else {
+					chosenMutation = allMutations.get(world.rand.nextInt(allMutations.size()));
+				}
+
+				ItemStack researchNote = AlleleManager.alleleRegistry.getMutationNoteStack(researcher, chosenMutation);
+				return new ItemStack[]{researchNote};
 			}
 		}
 
-		if (research != null) {
-			return new ItemStack[]{research};
-		} else {
-			return ItemStackUtil.EMPTY_STACK_ARRAY;
-		}
+		return ItemStackUtil.EMPTY_STACK_ARRAY;
 	}
 
 	@Override

src/main/java/forestry/core/genetics/mutations/Mutation.java

@@ -14,13 +14,6 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
-import net.minecraftforge.common.BiomeDictionary;
-
 import forestry.api.core.EnumHumidity;
 import forestry.api.core.EnumTemperature;
 import forestry.api.genetics.IAllele;
@@ -29,6 +22,10 @@ import forestry.api.genetics.IGenome;
 import forestry.api.genetics.IMutation;
 import forestry.api.genetics.IMutationBuilder;
 import forestry.api.genetics.IMutationCondition;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
+import net.minecraftforge.common.BiomeDictionary;
 
 public abstract class Mutation implements IMutation, IMutationBuilder {
 
@@ -109,14 +106,14 @@ public abstract class Mutation implements IMutation, IMutationBuilder {
 	}
 
 	@Override
-	public Mutation requireResource(IBlockState blockState) {
-		IMutationCondition mutationCondition = new MutationConditionRequiresResource(blockState);
+	public Mutation requireResource(IBlockState... acceptedBlockStates) {
+		IMutationCondition mutationCondition = new MutationConditionRequiresResource(acceptedBlockStates);
 		return addMutationCondition(mutationCondition);
 	}
 
 	@Override
 	public Mutation requireResource(String oreName) {
-		IMutationCondition mutationCondition = new MutationConditionRequiresResourceOreDict(oreName);
+		IMutationCondition mutationCondition = new MutationConditionRequiresResource(oreName);
 		return addMutationCondition(mutationCondition);
 	}
 

src/main/java/forestry/core/genetics/mutations/MutationConditionRequiresResource.java

@@ -10,38 +10,63 @@
  ******************************************************************************/
 package forestry.core.genetics.mutations;
 
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
 
 import forestry.api.apiculture.IBeeHousing;
 import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IGenome;
 import forestry.api.genetics.IMutationCondition;
-import forestry.core.utils.ItemStackUtil;
 import forestry.core.utils.Translator;
+import net.minecraft.block.Block;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.tileentity.TileEntity;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
+import net.minecraftforge.oredict.OreDictionary;
 
 public class MutationConditionRequiresResource implements IMutationCondition {
 
-	private final IBlockState requiredBlockState;
+	private final Set<IBlockState> acceptedBlockStates = new HashSet<>();
+	private final String displayName;
 
-	public MutationConditionRequiresResource(IBlockState requiredBlockState) {
-		this.requiredBlockState = requiredBlockState;
+	public MutationConditionRequiresResource(String oreDictName) {
+		this.displayName = oreDictName;
+		for (ItemStack ore : OreDictionary.getOres(oreDictName)) {
+			if (ore != null) {
+				Item oreItem = ore.getItem();
+				if (oreItem != null) {
+					Block oreBlock = Block.getBlockFromItem(oreItem);
+					if (oreBlock != null) {
+						this.acceptedBlockStates.addAll(oreBlock.getBlockState().getValidStates());
+					}
+				}
+			}
+		}
+	}
+
+	public MutationConditionRequiresResource(IBlockState... acceptedBlockStates) {
+		Collections.addAll(this.acceptedBlockStates, acceptedBlockStates);
+		this.displayName = acceptedBlockStates[0].getBlock().getLocalizedName();
 	}
 
 	@Override
 	public float getChance(World world, BlockPos pos, IAllele allele0, IAllele allele1, IGenome genome0, IGenome genome1) {
-		IBlockState blockState;
+		TileEntity tile;
 		do {
 			pos = pos.down();
-			blockState = world.getBlockState(pos);
-		} while (blockState.getBlock() instanceof IBeeHousing);
+			tile = world.getTileEntity(pos);
+		} while (tile instanceof IBeeHousing);
 
-		return this.requiredBlockState == blockState ? 1 : 0;
+		IBlockState blockState = world.getBlockState(pos);
+		return this.acceptedBlockStates.contains(blockState) ? 1 : 0;
 	}
 
 	@Override
 	public String getDescription() {
-		return Translator.translateToLocalFormatted("for.mutation.condition.resource", requiredBlockState.getBlock().getLocalizedName());
+		return Translator.translateToLocalFormatted("for.mutation.condition.resource", displayName);
 	}
 }

src/main/java/forestry/core/genetics/mutations/MutationConditionRequiresResourceOreDict.java

@@ -1,71 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2011-2014 SirSengir.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the GNU Lesser Public License v3
- * which accompanies this distribution, and is available at
- * http://www.gnu.org/licenses/lgpl-3.0.txt
- *
- * Various Contributors including, but not limited to:
- * SirSengir (original work), CovertJaguar, Player, Binnie, MysteriousAges
- ******************************************************************************/
-package forestry.core.genetics.mutations;
-
-import java.util.List;
-
-import net.minecraft.block.Block;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.item.ItemStack;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
-import net.minecraftforge.oredict.OreDictionary;
-
-import forestry.api.apiculture.IBeeHousing;
-import forestry.api.genetics.IAllele;
-import forestry.api.genetics.IGenome;
-import forestry.api.genetics.IMutationCondition;
-import forestry.core.utils.Translator;
-
-public class MutationConditionRequiresResourceOreDict implements IMutationCondition {
-
-	private final int oreDictId;
-	private final String displayName;
-
-	public MutationConditionRequiresResourceOreDict(String oreDictName) {
-		this.oreDictId = OreDictionary.getOreID(oreDictName);
-
-		List<ItemStack> ores = OreDictionary.getOres(oreDictName);
-		if (ores != null && !ores.isEmpty()) {
-			this.displayName = ores.get(0).getDisplayName();
-		} else {
-			this.displayName = oreDictName;
-		}
-	}
-
-	@Override
-	public float getChance(World world, BlockPos pos, IAllele allele0, IAllele allele1, IGenome genome0, IGenome genome1) {
-		Block block;
-		int meta;
-		int i = 1;
-		do {
-			BlockPos blockPos = new BlockPos(pos.getX(), pos.getY() - i, pos.getY());
-			IBlockState blockState = world.getBlockState(blockPos);
-			block = blockState.getBlock();
-			meta = block.getMetaFromState(blockState);
-			i++;
-		} while (block instanceof IBeeHousing);
-
-		int[] oreIds = OreDictionary.getOreIDs(new ItemStack(block, 1, meta));
-		for (int oreId : oreIds) {
-			if (oreId == this.oreDictId) {
-				return 1;
-			}
-		}
-		return 0;
-	}
-
-	@Override
-	public String getDescription() {
-		return Translator.translateToLocalFormatted("for.mutation.condition.resource", displayName);
-	}
-}

src/main/java/forestry/core/gui/ContainerEscritoire.java

@@ -23,16 +23,11 @@ import forestry.core.tiles.EscritoireGame;
 import forestry.core.tiles.TileEscritoire;
 
 public class ContainerEscritoire extends ContainerTile<TileEscritoire> implements IGuiSelectable {
-
-	private final EntityPlayer player;
-
 	private long lastUpdate;
 
 	public ContainerEscritoire(EntityPlayer player, TileEscritoire tile) {
 		super(tile, player.inventory, 34, 153);
 
-		this.player = player;
-
 		// Analyze slot
 		addSlotToContainer(new SlotFiltered(this.tile, InventoryEscritoire.SLOT_ANALYZE, 97, 67).setPickupWatcher(this.tile).setStackLimit(1));
 
@@ -54,7 +49,7 @@ public class ContainerEscritoire extends ContainerTile<TileEscritoire> implement
 		long gameLastUpdate = tile.getGame().getLastUpdate();
 		if (lastUpdate != gameLastUpdate) {
 			lastUpdate = gameLastUpdate;
-			Proxies.net.sendToPlayer(new PacketGuiUpdate(tile), player);
+			sendPacketToListeners(new PacketGuiUpdate(tile));
 		}
 	}
 

src/main/java/forestry/core/gui/slots/SlotWorking.java

@@ -31,7 +31,7 @@ public class SlotWorking extends SlotForestry {
 	}
 
 	@Override
-	public boolean getHasStack() {
+	public boolean canTakeStack(EntityPlayer stack) {
 		return false;
 	}
 

src/main/java/forestry/core/gui/widgets/GameTokenWidget.java

@@ -91,6 +91,7 @@ public class GameTokenWidget extends Widget {
 
 	@Override
 	public void handleMouseClick(int mouseX, int mouseY, int mouseButton) {
+		game.choose(index);
 		Proxies.net.sendToServer(new PacketGuiSelectRequest(index, 0));
 	}
 }

src/main/java/forestry/core/tiles/EscritoireGameBoard.java

@@ -17,6 +17,7 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Random;
 
+import forestry.api.genetics.IAllele;
 import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.nbt.NBTTagList;
@@ -72,10 +73,10 @@ public class EscritoireGameBoard implements INbtWritable, IStreamable {
 		tokenCount = getTokenCount(genome);
 
 		for (int i = 0; i < tokenCount / 2; i++) {
-			IIndividual token = root.templateAsIndividual(root.getRandomTemplate(rand));
-			ItemStack pair = root.getMemberStack(token, root.getIconType());
-			gameTokens.add(new EscritoireGameToken(pair));
-			gameTokens.add(new EscritoireGameToken(pair));
+			IAllele[] randomTemplate = root.getRandomTemplate(rand);
+			String speciesUid = randomTemplate[root.getSpeciesChromosomeType().ordinal()].getUID();
+			gameTokens.add(new EscritoireGameToken(speciesUid));
+			gameTokens.add(new EscritoireGameToken(speciesUid));
 		}
 		Collections.shuffle(gameTokens);
 		return true;

src/main/java/forestry/core/tiles/EscritoireGameToken.java

@@ -14,17 +14,19 @@ import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.io.IOException;
 
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-
 import forestry.api.core.INbtWritable;
 import forestry.api.genetics.AlleleManager;
+import forestry.api.genetics.IAllele;
+import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IIndividual;
+import forestry.api.genetics.ISpeciesRoot;
 import forestry.core.network.DataInputStreamForestry;
 import forestry.core.network.DataOutputStreamForestry;
 import forestry.core.network.IStreamable;
 import forestry.core.utils.ColourUtil;
 import forestry.core.utils.Translator;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
 
 public class EscritoireGameToken implements INbtWritable, IStreamable {
 
@@ -41,6 +43,8 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	private static final String[] OVERLAY_FAILED = new String[]{"errors/errored"};
 	private static final String[] OVERLAY_SELECTED = new String[]{"errors/unknown"};
 
+	@Nullable
+	private IIndividual tokenIndividual;
 	@Nullable
 	private ItemStack tokenStack;
 	@Nonnull
@@ -51,8 +55,8 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 		// required for IStreamable serialization
 	}
 
-	public EscritoireGameToken(@Nullable ItemStack tokenStack) {
-		this.tokenStack = tokenStack;
+	public EscritoireGameToken(@Nullable String speciesUid) {
+		setTokenSpecies(speciesUid);
 	}
 
 	public EscritoireGameToken(@Nonnull NBTTagCompound nbttagcompound) {
@@ -61,8 +65,29 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 			state = State.values()[stateOrdinal];
 		}
 
+		// legacy
 		if (nbttagcompound.hasKey("tokenStack")) {
 			tokenStack = ItemStack.loadItemStackFromNBT(nbttagcompound.getCompoundTag("tokenStack"));
+			ISpeciesRoot speciesRoot = AlleleManager.alleleRegistry.getSpeciesRoot(tokenStack);
+			tokenIndividual = speciesRoot.getMember(tokenStack);
+		}
+
+		if (nbttagcompound.hasKey("tokenSpecies")) {
+			String speciesUid = nbttagcompound.getString("tokenSpecies");
+			setTokenSpecies(speciesUid);
+		}
+	}
+
+	private void setTokenSpecies(String speciesUid) {
+		IAllele allele = AlleleManager.alleleRegistry.getAllele(speciesUid);
+		if (allele instanceof IAlleleSpecies) {
+			IAlleleSpecies species = (IAlleleSpecies) allele;
+			ISpeciesRoot root = species.getRoot();
+			IAllele[] template = root.getTemplate(speciesUid);
+			if (template != null) {
+				this.tokenIndividual = root.templateAsIndividual(template);
+				this.tokenStack = root.getMemberStack(this.tokenIndividual, root.getIconType());
+			}
 		}
 	}
 
@@ -108,12 +133,11 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	}
 
 	public int getTokenColour() {
-		if (tokenStack == null || !isVisible()) {
+		if (tokenIndividual == null || !isVisible()) {
 			return 0xffffff;
 		}
 
-		IIndividual individual = AlleleManager.alleleRegistry.getIndividual(tokenStack);
-		int iconColor = individual.getGenome().getPrimary().getSpriteColour(0);
+		int iconColor = tokenIndividual.getGenome().getPrimary().getSpriteColour(0);
 
 		if (state == State.MATCHED) {
 			return ColourUtil.multiplyRGBComponents(iconColor, 0.7f);
@@ -146,10 +170,8 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	public NBTTagCompound writeToNBT(NBTTagCompound nbttagcompound) {
 		nbttagcompound.setInteger("state", state.ordinal());
 
-		if (tokenStack != null) {
-			NBTTagCompound stackcompound = new NBTTagCompound();
-			tokenStack.writeToNBT(stackcompound);
-			nbttagcompound.setTag("tokenStack", stackcompound);
+		if (tokenIndividual != null) {
+			nbttagcompound.setString("tokenSpecies", tokenIndividual.getGenome().getPrimary().getUID());
 		}
 		return nbttagcompound;
 	}
@@ -158,12 +180,20 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	@Override
 	public void writeData(DataOutputStreamForestry data) throws IOException {
 		data.writeEnum(state, State.VALUES);
-		data.writeItemStack(tokenStack);
+		if (tokenIndividual != null) {
+			data.writeBoolean(true);
+			data.writeUTF(tokenIndividual.getGenome().getPrimary().getUID());
+		} else {
+			data.writeBoolean(false);
+		}
 	}
 
 	@Override
 	public void readData(DataInputStreamForestry data) throws IOException {
 		state = data.readEnum(State.VALUES);
-		tokenStack = data.readItemStack();
+		if (data.readBoolean()) {
+			String speciesUid = data.readUTF();
+			setTokenSpecies(speciesUid);
+		}
 	}
 }

src/main/java/forestry/core/utils/ItemStackUtil.java

@@ -423,9 +423,15 @@ public abstract class ItemStackUtil {
 	}
 
 	public static ItemStack copyWithRandomSize(ItemStack template, int max, Random rand) {
-		int size = rand.nextInt(max);
+		int size = max <= 0 ? 0 : rand.nextInt(max);
 		ItemStack created = template.copy();
-		created.stackSize = size <= 0 ? 1 : size > created.getMaxStackSize() ? created.getMaxStackSize() : size;
+		if (size <= 0) {
+			created.stackSize = 1;
+		} else if (size > created.getMaxStackSize()) {
+			created.stackSize = created.getMaxStackSize();
+		} else {
+			created.stackSize = size;
+		}
 		return created;
 	}
 

src/main/java/forestry/core/utils/OreDictUtil.java

@@ -36,6 +36,7 @@ public class OreDictUtil {
 	public static final String DOOR_WOOD = "doorWood";
 	public static final String TRAPDOOR_WOOD = "trapdoorWood";
 	public static final String TREE_LEAVES = "treeLeaves";
+	public static final String CHARCOAL = "itemCharcoal";
 
 	public static final String EMPTIED_LETTER_ORE_DICT = "emptiedLetter";
 

src/main/java/forestry/factory/PluginFactory.java

@@ -270,6 +270,7 @@ public class PluginFactory extends BlankForestryPlugin {
 		RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(Items.WHEAT_SEEDS)}, seedOil);
 		RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(Items.PUMPKIN_SEEDS)}, seedOil);
 		RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(Items.MELON_SEEDS)}, seedOil);
+		RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(Items.BEETROOT_SEEDS)}, seedOil);
 		RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{PluginCore.items.phosphor.getItemStack(2), new ItemStack(Blocks.COBBLESTONE)}, new FluidStack(FluidRegistry.LAVA, 1600));
 		RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(Blocks.CACTUS)}, new FluidStack(FluidRegistry.WATER, 500));
 		RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(Items.SNOWBALL), PluginCore.items.craftingMaterial.getIceShard(4)}, Fluids.ICE.getFluid(4000));

src/main/java/forestry/factory/recipes/jei/WorktableRecipeTransferHandler.java

@@ -6,19 +6,17 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
-import net.minecraft.entity.player.EntityPlayer;
-import net.minecraft.inventory.Container;
-import net.minecraft.item.ItemStack;
-
 import forestry.factory.gui.ContainerWorktable;
 import forestry.factory.inventory.InventoryCraftingForestry;
 import forestry.factory.recipes.MemorizedRecipe;
-
+import mezz.jei.api.gui.IGuiIngredient;
 import mezz.jei.api.gui.IRecipeLayout;
 import mezz.jei.api.recipe.VanillaRecipeCategoryUid;
 import mezz.jei.api.recipe.transfer.IRecipeTransferError;
 import mezz.jei.api.recipe.transfer.IRecipeTransferHandler;
-import mezz.jei.gui.ingredients.IGuiIngredient;
+import net.minecraft.entity.player.EntityPlayer;
+import net.minecraft.inventory.Container;
+import net.minecraft.item.ItemStack;
 
 class WorktableRecipeTransferHandler implements IRecipeTransferHandler {
 	@Override

src/main/java/forestry/lepidopterology/genetics/ButterflyGenome.java

@@ -10,8 +10,6 @@
  ******************************************************************************/
 package forestry.lepidopterology.genetics;
 
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
 import forestry.api.genetics.EnumTolerance;
 import forestry.api.genetics.IAlleleFloat;
 import forestry.api.genetics.IAlleleFlowers;
@@ -29,6 +27,8 @@ import forestry.api.lepidopterology.IButterflyGenome;
 import forestry.core.genetics.Genome;
 import forestry.core.genetics.alleles.AlleleBoolean;
 import forestry.core.genetics.alleles.AlleleTolerance;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
 
 public class ButterflyGenome extends Genome implements IButterflyGenome {
 
@@ -46,8 +46,8 @@ public class ButterflyGenome extends Genome implements IButterflyGenome {
 		if (!ButterflyManager.butterflyRoot.isMember(itemStack)) {
 			return null;
 		}
-		
-		IAlleleSpecies species = getSpeciesDirectly(itemStack);
+
+		IAlleleSpecies species = getSpeciesDirectly(ButterflyManager.butterflyRoot, itemStack);
 		if (species instanceof IAlleleButterflySpecies) {
 			return (IAlleleButterflySpecies) species;
 		}

src/main/java/forestry/lepidopterology/genetics/ButterflyRoot.java

@@ -12,21 +12,11 @@ package forestry.lepidopterology.genetics;
 
 import javax.annotation.Nullable;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Collections;
+import java.util.List;
 import java.util.Map.Entry;
 
-import net.minecraft.block.Block;
-import net.minecraft.block.state.IBlockState;
-import net.minecraft.item.Item;
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-import net.minecraft.tileentity.TileEntity;
-import net.minecraft.util.math.BlockPos;
-import net.minecraft.world.World;
-
 import com.mojang.authlib.GameProfile;
-
 import forestry.api.genetics.AlleleManager;
 import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IAlyzerPlugin;
@@ -50,6 +40,14 @@ import forestry.core.utils.EntityUtil;
 import forestry.lepidopterology.PluginLepidopterology;
 import forestry.lepidopterology.entities.EntityButterfly;
 import forestry.lepidopterology.tiles.TileCocoon;
+import net.minecraft.block.Block;
+import net.minecraft.block.state.IBlockState;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.tileentity.TileEntity;
+import net.minecraft.util.math.BlockPos;
+import net.minecraft.world.World;
 
 public class ButterflyRoot extends SpeciesRoot implements IButterflyRoot {
 
@@ -266,7 +264,7 @@ public class ButterflyRoot extends SpeciesRoot implements IButterflyRoot {
 	}
 
 	/* MUTATIONS */
-	private static final ArrayList<IButterflyMutation> butterflyMutations = new ArrayList<>();
+	private static final List<IButterflyMutation> butterflyMutations = new ArrayList<>();
 
 	@Override
 	public void registerMutation(IMutation mutation) {
@@ -284,7 +282,7 @@ public class ButterflyRoot extends SpeciesRoot implements IButterflyRoot {
 	}
 
 	@Override
-	public Collection<IButterflyMutation> getMutations(boolean shuffle) {
+	public List<IButterflyMutation> getMutations(boolean shuffle) {
 		if (shuffle) {
 			Collections.shuffle(butterflyMutations);
 		}
@@ -315,7 +313,7 @@ public class ButterflyRoot extends SpeciesRoot implements IButterflyRoot {
 	}
 
 	@Override
-	public IChromosomeType getKaryotypeKey() {
+	public IChromosomeType getSpeciesChromosomeType() {
 		return EnumButterflyChromosome.SPECIES;
 	}
 

src/main/java/forestry/lepidopterology/genetics/MothDefinition.java

@@ -33,7 +33,7 @@ import forestry.lepidopterology.genetics.alleles.AlleleButterflyCocoon;
 
 public enum MothDefinition implements IButterflyDefinition {
 	Brimstone(ButterflyBranchDefinition.Opisthograptis, "brimstone", "luteolata", new Color(0xffea40), true, 1.0f),
-	LatticedHeath(ButterflyBranchDefinition.Chiasmia, "latticeHeath", "clathrata", new Color(0xf2f0be), true, 0.5f) {
+	LatticedHeath(ButterflyBranchDefinition.Chiasmia, "latticedHeath", "clathrata", new Color(0xf2f0be), true, 0.5f) {
 		@Override
 		protected void setAlleles(IAllele[] alleles) {
 			AlleleHelper.instance.set(alleles, EnumButterflyChromosome.SIZE, EnumAllele.Size.SMALLEST);

src/main/java/forestry/storage/BackpackMode.java

@@ -15,8 +15,8 @@ import javax.annotation.Nullable;
 public enum BackpackMode {
 	NORMAL(null),
 	LOCKED("for.storage.backpack.mode.locked"),
-	RECEIVE("for.storage.backpack.mode.locked"),
-	RESUPPLY("for.storage.backpack.mode.locked");
+	RECEIVE("for.storage.backpack.mode.receiving"),
+	RESUPPLY("for.storage.backpack.mode.resupply");
 
 	@Nullable
 	private final String unlocalizedInfo;