Merge branch 'dev' into inventory-cleanup

src/main/java/forestry/apiculture/VillageHandlerApiculture.java

@@ -10,9 +10,17 @@
  ******************************************************************************/
 package forestry.apiculture;
 
-import java.util.List;
-import java.util.Random;
-
+import cpw.mods.fml.common.registry.VillagerRegistry.IVillageCreationHandler;
+import cpw.mods.fml.common.registry.VillagerRegistry.IVillageTradeHandler;
+import forestry.api.apiculture.EnumBeeType;
+import forestry.apiculture.genetics.BeeTemplates;
+import forestry.apiculture.items.ItemHoneycomb;
+import forestry.apiculture.worldgen.ComponentVillageBeeHouse;
+import forestry.core.config.Defaults;
+import forestry.core.config.ForestryBlock;
+import forestry.core.config.ForestryItem;
+import forestry.core.proxy.Proxies;
+import forestry.plugins.PluginApiculture;
 import net.minecraft.entity.passive.EntityVillager;
 import net.minecraft.init.Blocks;
 import net.minecraft.init.Items;
@@ -23,17 +31,8 @@ import net.minecraft.village.MerchantRecipeList;
 import net.minecraft.world.gen.structure.MapGenStructureIO;
 import net.minecraft.world.gen.structure.StructureVillagePieces;
 
-import cpw.mods.fml.common.registry.VillagerRegistry.IVillageCreationHandler;
-import cpw.mods.fml.common.registry.VillagerRegistry.IVillageTradeHandler;
-
-import forestry.api.apiculture.EnumBeeType;
-import forestry.apiculture.genetics.BeeTemplates;
-import forestry.apiculture.items.ItemHoneycomb;
-import forestry.apiculture.worldgen.ComponentVillageBeeHouse;
-import forestry.core.config.Defaults;
-import forestry.core.config.ForestryBlock;
-import forestry.core.config.ForestryItem;
-import forestry.plugins.PluginApiculture;
+import java.util.List;
+import java.util.Random;
 
 public class VillageHandlerApiculture implements IVillageCreationHandler, IVillageTradeHandler {
 
@@ -41,6 +40,7 @@ public class VillageHandlerApiculture implements IVillageCreationHandler, IVilla
 		try {
 			MapGenStructureIO.func_143031_a(ComponentVillageBeeHouse.class, "Forestry:BeeHouse");
 		} catch (Throwable e) {
+			Proxies.log.severe("Failed to register village beehouse.");
 		}
 	}
 

src/main/java/forestry/apiculture/gadgets/BlockAlveary.java

@@ -105,13 +105,13 @@ public class BlockAlveary extends BlockStructure {
 	public static final int BOTTOM = 2;
 	public static final int LEFT = 3;
 	public static final int RIGHT = 4;
-	public static final int TX_55_SWOF = 5;
-	public static final int TX_56_SWON = 6;
-	public static final int TX_57_HTOF = 7;
-	public static final int TX_58_HTON = 8;
-	public static final int TX_71_FNOF = 9;
-	public static final int TX_72_FNON = 10;
-	public static final int TX_73_VLVE = 11;
+	public static final int ALVEARY_SWARMER_OFF = 5;
+	public static final int ALVEARY_SWARMER_ON = 6;
+	public static final int ALVEARY_HEATER_OFF = 7;
+	public static final int ALVEARY_HEATER_ON = 8;
+	public static final int ALVEARY_FAN_OFF = 9;
+	public static final int ALVEARY_FAN_ON = 10;
+	public static final int ALVEARY_HYGRO = 11;
 	public static final int STABILISER = 12;
 	public static final int SIEVE = 13;
 
@@ -152,13 +152,13 @@ public class BlockAlveary extends BlockStructure {
 		case 1:
 			return icons[ENTRANCE];
 		case TileAlvearySwarmer.BLOCK_META:
-			return icons[TX_55_SWOF];
+			return icons[ALVEARY_SWARMER_OFF];
 		case TileAlvearyFan.BLOCK_META:
-			return icons[TX_71_FNOF];
+			return icons[ALVEARY_FAN_OFF];
 		case TileAlvearyHeater.BLOCK_META:
-			return icons[TX_57_HTOF];
+			return icons[ALVEARY_HEATER_OFF];
 		case TileAlvearyHygroregulator.BLOCK_META:
-			return icons[TX_73_VLVE];
+			return icons[ALVEARY_HYGRO];
 		case TileAlvearyStabiliser.BLOCK_META:
 			return icons[STABILISER];
 		case TileAlvearySieve.BLOCK_META:

src/main/java/forestry/apiculture/gadgets/TileAlvearyClimatiser.java

@@ -34,15 +34,14 @@ public abstract class TileAlvearyClimatiser extends TileAlveary implements IEner
 	}
 	protected final EnergyManager energyManager;
 	private final ClimateControl climateControl;
-	private int transferTime = 0;
-	private int animationDelay = 0;
+	private int workingTime = 0;
 	private final int textureOff;
 	private final int textureOn;
 
 	public TileAlvearyClimatiser(ClimateControl control, int textureOff, int textureOn, int componentBlockMeta) {
 		super(componentBlockMeta);
 		this.climateControl = control;
-		energyManager = new EnergyManager(1000, 250, 2000);
+		energyManager = new EnergyManager(1000, 50, 2000);
 		energyManager.setReceiveOnly();
 		this.textureOff = textureOff;
 		this.textureOn = textureOn;
@@ -60,28 +59,22 @@ public abstract class TileAlvearyClimatiser extends TileAlveary implements IEner
 		if (!this.hasMaster())
 			return;
 
-		if (energyManager.consumeEnergyToDoWork()) {
+		boolean wasInactive = (workingTime == 0);
 
-			transferTime = energyManager.getEnergyPerWork();
-
-			if (animationDelay <= 0) {
-				animationDelay = 100;
-				sendNetworkUpdate();
-			} else
-				animationDelay = 100;
+		if (workingTime < 20 && energyManager.consumeEnergyToDoWork()) {
+			// consume 10 RF per tick of work
+			workingTime += energyManager.getEnergyPerWork() / 10;
 		}
 
-		if (transferTime > 0) {
-			transferTime--;
+		if (workingTime > 0) {
+			workingTime--;
 			IAlvearyComponent component = (IAlvearyComponent) this.getCentralTE();
 			if (component != null)
 				component.addTemperatureChange(climateControl.changePerTransfer, climateControl.boundaryDown, climateControl.boundaryUp);
 		}
 
-		if (animationDelay > 0) {
-			animationDelay--;
-			if (animationDelay <= 0)
-				sendNetworkUpdate();
+		if ((wasInactive && workingTime > 0) || (!wasInactive && workingTime == 0)) {
+			sendNetworkUpdate();
 		}
 	}
 
@@ -93,7 +86,7 @@ public abstract class TileAlvearyClimatiser extends TileAlveary implements IEner
 	/* TEXTURES */
 	@Override
 	public int getIcon(int side, int metadata) {
-		if (animationDelay > 0)
+		if (workingTime > 0)
 			return textureOn;
 		else
 			return textureOff;
@@ -104,23 +97,23 @@ public abstract class TileAlvearyClimatiser extends TileAlveary implements IEner
 	public void readFromNBT(NBTTagCompound nbttagcompound) {
 		super.readFromNBT(nbttagcompound);
 		energyManager.readFromNBT(nbttagcompound);
-		transferTime = nbttagcompound.getInteger("Heating");
+		workingTime = nbttagcompound.getInteger("Heating");
 	}
 
 	@Override
 	public void writeToNBT(NBTTagCompound nbttagcompound) {
 		super.writeToNBT(nbttagcompound);
 		energyManager.writeToNBT(nbttagcompound);
-		nbttagcompound.setInteger("Heating", transferTime);
+		nbttagcompound.setInteger("Heating", workingTime);
 	}
 
 
 	/* NETWORK */
 	@Override
 	public void fromPacketPayload(PacketPayload payload) {
-		short delay = payload.shortPayload[0];
-		if (animationDelay != delay) {
-			animationDelay = delay;
+		short workingTime = payload.shortPayload[0];
+		if (this.workingTime != workingTime) {
+			this.workingTime = workingTime;
 			worldObj.func_147479_m(xCoord, yCoord, zCoord);
 		}
 	}
@@ -128,7 +121,7 @@ public abstract class TileAlvearyClimatiser extends TileAlveary implements IEner
 	@Override
 	public PacketPayload getPacketPayload() {
 		PacketPayload payload = new PacketPayload(0, 1);
-		payload.shortPayload[0] = (short) animationDelay;
+		payload.shortPayload[0] = (short) workingTime;
 		return payload;
 	}
 

src/main/java/forestry/apiculture/gadgets/TileAlvearyFan.java

@@ -16,7 +16,7 @@ public class TileAlvearyFan extends TileAlvearyClimatiser {
 	public static final int BLOCK_META = 3;
 
 	public TileAlvearyFan() {
-		super(new ClimateControl(-0.01f, 0.05f, 2.5f), BlockAlveary.TX_71_FNOF, BlockAlveary.TX_72_FNON, BLOCK_META);
+		super(new ClimateControl(-0.01f, 0.05f, 2.5f), BlockAlveary.ALVEARY_FAN_OFF, BlockAlveary.ALVEARY_FAN_ON, BLOCK_META);
 	}
 
 }

src/main/java/forestry/apiculture/gadgets/TileAlvearyHeater.java

@@ -12,14 +12,11 @@ package forestry.apiculture.gadgets;
 
 public class TileAlvearyHeater extends TileAlvearyClimatiser {
 
-	public static final int TEXTURE_OFF = 57;
-	public static final int TEXTURE_ON = 58;
-
 	/* CONSTANTS */
 	public static final int BLOCK_META = 4;
 
 	public TileAlvearyHeater() {
-		super(new ClimateControl(0.01f, 0.0f, 2.5f), BlockAlveary.TX_57_HTOF, BlockAlveary.TX_58_HTON, BLOCK_META);
+		super(new ClimateControl(0.01f, 0.0f, 2.5f), BlockAlveary.ALVEARY_HEATER_OFF, BlockAlveary.ALVEARY_HEATER_ON, BLOCK_META);
 	}
 
 }

src/main/java/forestry/apiculture/gadgets/TileAlvearyHygroregulator.java

@@ -187,7 +187,7 @@ public class TileAlvearyHygroregulator extends TileAlveary implements IInventory
 	/* TEXTURES */
 	@Override
 	public int getIcon(int side, int metadata) {
-		return BlockAlveary.TX_73_VLVE;
+		return BlockAlveary.ALVEARY_HYGRO;
 	}
 
 	@Override

src/main/java/forestry/apiculture/gadgets/TileAlvearyPlain.java

@@ -83,6 +83,17 @@ public class TileAlvearyPlain extends TileAlveary implements ISidedInventory, IS
 			player.openGui(ForestryAPI.instance, GuiId.AlvearyGUI.ordinal(), worldObj, masterX, masterY, masterZ);
 	}
 
+	@Override
+	public void validate() {
+		super.validate();
+		setBiomeInformation();
+	}
+
+	private void setBiomeInformation() {
+		this.biome = Utils.getBiomeAt(worldObj, xCoord, zCoord);
+		setErrorState(EnumErrorCode.OK);
+	}
+
 	/* LOADING & SAVING */
 	@Override
 	public void readFromNBT(NBTTagCompound nbttagcompound) {
@@ -112,8 +123,7 @@ public class TileAlvearyPlain extends TileAlveary implements ISidedInventory, IS
 	@Override
 	public void initialize() {
 		super.initialize();
-		this.biome = Utils.getBiomeAt(worldObj, xCoord, zCoord);
-		setErrorState(EnumErrorCode.OK);
+		setBiomeInformation();
 	}
 
 	@Override

src/main/java/forestry/apiculture/gadgets/TileAlvearySwarmer.java

@@ -163,9 +163,9 @@ public class TileAlvearySwarmer extends TileAlveary implements ISidedInventory {
 			return BlockAlveary.BOTTOM;
 
 		if (pendingSpawns.size() > 0)
-			return BlockAlveary.TX_56_SWON;
+			return BlockAlveary.ALVEARY_SWARMER_ON;
 		else
-			return BlockAlveary.TX_55_SWOF;
+			return BlockAlveary.ALVEARY_SWARMER_OFF;
 	}
 
 	/* SAVING & LOADING */

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

@@ -112,7 +112,7 @@ public class AlleleBeeSpecies extends AlleleSpecies implements IAlleleBeeSpecies
 		int highest = 0;
 		exclude.add(species);
 
-		for(IMutation mutation : getRoot().getPaths(species, EnumBeeChromosome.SPECIES.ordinal())) {
+		for(IMutation mutation : getRoot().getPaths(species, EnumBeeChromosome.SPECIES)) {
 			if(!exclude.contains(mutation.getAllele0())) {
 				int otherAdvance = getGeneticAdvancement(mutation.getAllele0(), exclude);
 				if(otherAdvance > highest)

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

@@ -0,0 +1,59 @@
+package forestry.apiculture.genetics;
+
+import java.util.Random;
+import net.minecraft.block.Block;
+import net.minecraft.world.World;
+import forestry.api.apiculture.IBeeGenome;
+import forestry.api.apiculture.IBeeHousing;
+import forestry.api.genetics.IEffectData;
+
+public class AlleleEffectFertile extends AlleleEffectThrottled {
+	
+	public static final int MAX_BLOCK_FIND_TRIES = 5;
+
+	public AlleleEffectFertile(String uid) {
+		super(uid, "fertile", false, 6, true, false);
+	}
+
+	@Override
+	public IEffectData doEffect(IBeeGenome genome, IEffectData storedData, IBeeHousing housing) {
+		
+		if (isHalted(storedData, housing)) {
+			return storedData;
+		}
+		
+		World world = housing.getWorld();
+		int territorySize[] = genome.getTerritory();
+		
+		int blockX = getRandomOffset(world.rand, housing.getXCoord(), territorySize[0]);
+		int blockZ = getRandomOffset(world.rand, housing.getZCoord(), territorySize[2]);
+		int blockMaxY = housing.getYCoord() + territorySize[1] / 2 + 1;
+		int blockMinY = housing.getYCoord() - (territorySize[1] / 2) - 1;
+		
+		for (int attempt = 0; attempt < MAX_BLOCK_FIND_TRIES; ++attempt) {
+			if (tryTickColumn(world, blockX, blockZ, blockMaxY, blockMinY)) {
+				break;
+			}
+			blockX = getRandomOffset(world.rand, housing.getXCoord(), territorySize[0]);
+			blockZ = getRandomOffset(world.rand, housing.getZCoord(), territorySize[2]);
+		}
+		
+		return storedData;
+	}
+	
+	private int getRandomOffset(Random random, int centrePos, int offset) {
+		return centrePos + random.nextInt(offset) - (offset / 2);
+	}
+
+	private boolean tryTickColumn(World world, int x, int z, int maxY, int minY) {
+		for (int y = maxY; y >= minY; --y) {
+			if (!world.isAirBlock(x, y, z)) {
+				Block block = world.getBlock(x, y, z);
+				world.scheduleBlockUpdate(x, y, z, block, 5);
+				return true;
+			}
+		}
+		return false;
+	}
+
+}

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

@@ -10,25 +10,25 @@
  ******************************************************************************/
 package forestry.apiculture.genetics;
 
-import java.util.List;
-
+import forestry.api.apiculture.IBeeGenome;
+import forestry.api.apiculture.IBeeHousing;
+import forestry.api.genetics.IEffectData;
+import forestry.apiculture.items.ItemArmorApiarist;
 import net.minecraft.entity.player.EntityPlayer;
 import net.minecraft.potion.Potion;
 import net.minecraft.potion.PotionEffect;
 import net.minecraft.util.AxisAlignedBB;
 
-import forestry.api.apiculture.IBeeGenome;
-import forestry.api.apiculture.IBeeHousing;
-import forestry.api.genetics.IEffectData;
+import java.util.List;
 
 public class AlleleEffectPotion extends AlleleEffectThrottled {
 
-	private int potionId = 0;
+	private final Potion potion;
 	private final int duration;
 
 	public AlleleEffectPotion(String uid, String name, boolean isDominant, Potion potion, int duration, boolean requiresWorking) {
 		super(uid, name, isDominant, 200, requiresWorking, false);
-		potionId = potion.getId();
+		this.potion = potion;
 		this.duration = duration;
 	}
 
@@ -39,12 +39,29 @@ public class AlleleEffectPotion extends AlleleEffectThrottled {
 			return storedData;
 
 		AxisAlignedBB beatifyBox = getBounding(genome, housing, 1.0f);
-		@SuppressWarnings("rawtypes")
 		List list = housing.getWorld().getEntitiesWithinAABB(EntityPlayer.class, beatifyBox);
 
-		for (Object obj : list) {
-			EntityPlayer player = (EntityPlayer) obj;
-			player.addPotionEffect(new PotionEffect(potionId, duration, 0));
+		for (Object entity : list) {
+			if (!(entity instanceof EntityPlayer))
+				continue;
+
+			EntityPlayer player = (EntityPlayer) entity;
+
+			int duration = this.duration;
+			if (potion.isBadEffect()) {
+				// Players are not attacked if they wear a full set of apiarist's armor.
+				int count = ItemArmorApiarist.wearsItems((EntityPlayer) entity, getUID(), true);
+				if (count >= 4)
+					continue; // Full set, no damage/effect
+				else if (count == 3)
+					duration = this.duration / 4;
+				else if (count == 2)
+					duration = this.duration / 2;
+				else if (count == 1)
+					duration = this.duration * 3 / 4;
+			}
+
+			player.addPotionEffect(new PotionEffect(potion.getId(), duration, 0));
 		}
 
 		return storedData;

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

@@ -10,16 +10,15 @@
  ******************************************************************************/
 package forestry.apiculture.genetics;
 
-import net.minecraft.entity.player.EntityPlayer;
-import net.minecraft.nbt.NBTTagCompound;
-
 import com.mojang.authlib.GameProfile;
-
+import forestry.api.apiculture.EnumBeeChromosome;
 import forestry.api.apiculture.IApiaristTracker;
 import forestry.api.genetics.IBreedingTracker;
 import forestry.api.genetics.IIndividual;
 import forestry.core.genetics.BreedingTracker;
 import forestry.plugins.PluginApiculture;
+import net.minecraft.entity.player.EntityPlayer;
+import net.minecraft.nbt.NBTTagCompound;
 
 public class ApiaristTracker extends BreedingTracker implements IApiaristTracker {
 
@@ -61,7 +60,7 @@ public class ApiaristTracker extends BreedingTracker implements IApiaristTracker
 	public void registerPickup(IIndividual individual) {
 		if(!individual.getGenome().getPrimary().getRoot().getUID().equals(BeeHelper.UID))
 			return;
-		if(!individual.isPureBred(0))
+		if(!individual.isPureBred(EnumBeeChromosome.SPECIES))
 			return;
 		if(PluginApiculture.beeInterface.getCombinations(individual.getGenome().getPrimary()).size() > 0)
 			return;

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

@@ -131,7 +131,7 @@ public class Bee extends IndividualLiving implements IBee {
 		if (!effect.isCombinable())
 			return storedData;
 
-		IAlleleBeeEffect secondary = (IAlleleBeeEffect) genome.getInactiveAllele(EnumBeeChromosome.EFFECT.ordinal());
+		IAlleleBeeEffect secondary = (IAlleleBeeEffect) genome.getInactiveAllele(EnumBeeChromosome.EFFECT);
 		if (!secondary.isCombinable())
 			return storedData;
 
@@ -158,7 +158,7 @@ public class Bee extends IndividualLiving implements IBee {
 		if (!effect.isCombinable())
 			return storedData;
 
-		IAlleleBeeEffect secondary = (IAlleleBeeEffect) genome.getInactiveAllele(EnumBeeChromosome.EFFECT.ordinal());
+		IAlleleBeeEffect secondary = (IAlleleBeeEffect) genome.getInactiveAllele(EnumBeeChromosome.EFFECT);
 		if (!secondary.isCombinable())
 			return storedData;
 
@@ -351,22 +351,22 @@ public class Bee extends IndividualLiving implements IBee {
 		// You analyzed it? Juicy tooltip coming up!
 		IAlleleBeeSpecies primary = genome.getPrimary();
 		IAlleleBeeSpecies secondary = genome.getSecondary();
-		if (!isPureBred(EnumBeeChromosome.SPECIES.ordinal()))
+		if (!isPureBred(EnumBeeChromosome.SPECIES))
 			list.add("\u00A79" + StringUtil.localize("bees.hybrid").replaceAll("%PRIMARY",primary.getName()).replaceAll("%SECONDARY",secondary.getName()));
 
-		IAllele speed = genome.getActiveAllele(EnumBeeChromosome.SPEED.ordinal());
+		IAllele speed = genome.getActiveAllele(EnumBeeChromosome.SPEED);
 		String customWorker = "tooltip.worker." + speed.getUnlocalizedName().replaceFirst("gui.", "");
 		if (StringUtil.canTranslate(customWorker))
 			list.add(StringUtil.localize(customWorker));
 		else
 			list.add(speed.getName() + " " + StringUtil.localize("gui.worker"));
 
-		list.add(genome.getActiveAllele(EnumBeeChromosome.LIFESPAN.ordinal()).getName() + " " + StringUtil.localize("gui.life"));
+		list.add(genome.getActiveAllele(EnumBeeChromosome.LIFESPAN).getName() + " " + StringUtil.localize("gui.life"));
 
-		IAlleleTolerance tempTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE.ordinal());
+		IAlleleTolerance tempTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE);
 		list.add("\u00A7aT: " + AlleleManager.climateHelper.toDisplay(genome.getPrimary().getTemperature()) + " / " + tempTolerance.getName());
 
-		IAlleleTolerance humidTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE.ordinal());
+		IAlleleTolerance humidTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE);
 		list.add("\u00A7aH: " + AlleleManager.climateHelper.toDisplay(genome.getPrimary().getHumidity()) + " / " + humidTolerance.getName());
 
 		list.add(genome.getFlowerProvider().getDescription());

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

@@ -82,73 +82,73 @@ public class BeeGenome extends Genome implements IBeeGenome {
 	// / INFORMATION RETRIEVAL
 	@Override
 	public IAlleleBeeSpecies getPrimary() {
-		return (IAlleleBeeSpecies) getActiveAllele(EnumBeeChromosome.SPECIES.ordinal());
+		return (IAlleleBeeSpecies) getActiveAllele(EnumBeeChromosome.SPECIES);
 	}
 
 	@Override
 	public IAlleleBeeSpecies getSecondary() {
-		return (IAlleleBeeSpecies) getInactiveAllele(EnumBeeChromosome.SPECIES.ordinal());
+		return (IAlleleBeeSpecies) getInactiveAllele(EnumBeeChromosome.SPECIES);
 	}
 
 	@Override
 	public float getSpeed() {
-		return ((IAlleleFloat) getActiveAllele(EnumBeeChromosome.SPEED.ordinal())).getValue();
+		return ((IAlleleFloat) getActiveAllele(EnumBeeChromosome.SPEED)).getValue();
 	}
 
 	@Override
 	public int getLifespan() {
-		return ((IAlleleInteger) getActiveAllele(EnumBeeChromosome.LIFESPAN.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumBeeChromosome.LIFESPAN)).getValue();
 	}
 
 	@Override
 	public int getFertility() {
-		return ((IAlleleInteger) getActiveAllele(EnumBeeChromosome.FERTILITY.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumBeeChromosome.FERTILITY)).getValue();
 	}
 
 	@Override
 	public EnumTolerance getToleranceTemp() {
-		return ((AlleleTolerance) getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE.ordinal())).getValue();
+		return ((AlleleTolerance) getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE)).getValue();
 	}
 
 	@Override
 	public boolean getNocturnal() {
-		return ((AlleleBoolean) getActiveAllele(EnumBeeChromosome.NOCTURNAL.ordinal())).getValue();
+		return ((AlleleBoolean) getActiveAllele(EnumBeeChromosome.NOCTURNAL)).getValue();
 	}
 
 	@Override
 	public EnumTolerance getToleranceHumid() {
-		return ((AlleleTolerance) getActiveAllele(EnumBeeChromosome.HUMIDITY_TOLERANCE.ordinal())).getValue();
+		return ((AlleleTolerance) getActiveAllele(EnumBeeChromosome.HUMIDITY_TOLERANCE)).getValue();
 	}
 
 	@Override
 	public boolean getTolerantFlyer() {
-		return ((AlleleBoolean) getActiveAllele(EnumBeeChromosome.TOLERANT_FLYER.ordinal())).getValue();
+		return ((AlleleBoolean) getActiveAllele(EnumBeeChromosome.TOLERANT_FLYER)).getValue();
 	}
 
 	@Override
 	public boolean getCaveDwelling() {
-		return ((AlleleBoolean) getActiveAllele(EnumBeeChromosome.CAVE_DWELLING.ordinal())).getValue();
+		return ((AlleleBoolean) getActiveAllele(EnumBeeChromosome.CAVE_DWELLING)).getValue();
 	}
 
 	@Override
 	public IFlowerProvider getFlowerProvider() {
-		return ((IAlleleFlowers) getActiveAllele(EnumBeeChromosome.FLOWER_PROVIDER.ordinal())).getProvider();
+		return ((IAlleleFlowers) getActiveAllele(EnumBeeChromosome.FLOWER_PROVIDER)).getProvider();
 	}
 
 	@Override
 	public int getFlowering() {
-		return ((IAlleleInteger) getActiveAllele(EnumBeeChromosome.FLOWERING.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumBeeChromosome.FLOWERING)).getValue();
 	}
 
 	@Override
 	public int[] getTerritory() {
-		Vect area = ((AlleleArea) getActiveAllele(EnumBeeChromosome.TERRITORY.ordinal())).getArea();
+		Vect area = ((AlleleArea) getActiveAllele(EnumBeeChromosome.TERRITORY)).getArea();
 		return new int[] { area.x, area.y, area.z };
 	}
 
 	@Override
 	public IAlleleBeeEffect getEffect() {
-		return (IAlleleBeeEffect) getActiveAllele(EnumBeeChromosome.EFFECT.ordinal());
+		return (IAlleleBeeEffect) getActiveAllele(EnumBeeChromosome.EFFECT);
 	}
 
 	@Override

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

@@ -548,6 +548,24 @@ public class BeeTemplates {
 		alleles[EnumBeeChromosome.SPECIES.ordinal()] = Allele.speciesRural;
 		return alleles;
 	}
+	
+	public static IAllele[] getFarmerlyTemplate() {
+		IAllele[] alleles = getAgrarianBranchTemplate();
+		alleles[EnumBeeChromosome.SPECIES.ordinal()] = Allele.speciesFarmerly;
+		alleles[EnumBeeChromosome.SPEED.ordinal()] = Allele.speedSlow;
+		alleles[EnumBeeChromosome.TERRITORY.ordinal()] = Allele.territoryLarge;
+		return alleles;
+	}
+	
+	public static IAllele[] getAgrarianTemplate() {
+		IAllele[] alleles = getAgrarianBranchTemplate();
+		alleles[EnumBeeChromosome.SPECIES.ordinal()] = Allele.speciesArgrarian;
+		alleles[EnumBeeChromosome.SPEED.ordinal()] = Allele.speedSlow;
+		alleles[EnumBeeChromosome.HUMIDITY_TOLERANCE.ordinal()] = Allele.toleranceBoth2;
+		alleles[EnumBeeChromosome.EFFECT.ordinal()] = Allele.effectFertile;
+		alleles[EnumBeeChromosome.TERRITORY.ordinal()] = Allele.territoryLarge;
+		return alleles;
+	}
 
 	// / BOGGY BRANCH
 	public static IAllele[] getBoggyBranchTemplate() {

src/main/java/forestry/apiculture/gui/GuiBeealyzer.java

@@ -12,7 +12,6 @@ package forestry.apiculture.gui;
 
 import forestry.api.apiculture.EnumBeeChromosome;
 import forestry.api.apiculture.EnumBeeType;
-import forestry.api.apiculture.IAlleleBeeEffect;
 import forestry.api.apiculture.IBee;
 import forestry.api.genetics.AlleleManager;
 import forestry.api.genetics.IAlleleFlowers;
@@ -35,13 +34,8 @@ import java.util.ArrayList;
 
 public class GuiBeealyzer extends GuiAlyzer {
 
-	private ItemStack[] tempProductList;
-
 	public GuiBeealyzer(EntityPlayer player, BeealyzerInventory inventory) {
-		super(AlleleManager.alleleRegistry.getSpeciesRoot("rootBees"), player,
-				new ContainerBeealyzer(player.inventory, inventory), inventory, 1, inventory.getSizeInventory());
-
-		guiName = "gui.beealyzer";
+		super("rootBees", player, new ContainerBeealyzer(player.inventory, inventory), inventory, "gui.beealyzer");
 
 		ArrayList<ItemStack> beeList = new ArrayList<ItemStack>();
 		((ItemBeeGE) ForestryItem.beeDroneGE.item()).addCreativeItems(beeList, false);
@@ -111,36 +105,36 @@ public class GuiBeealyzer extends GuiAlyzer {
 
 			drawSpeciesRow(StringUtil.localize("gui.species"), bee, EnumBeeChromosome.SPECIES, checkCustomName(customPrimaryBeeKey), checkCustomName(customSecondaryBeeKey));
 		}
-		drawRow(StringUtil.localize("gui.lifespan"), bee.getGenome().getActiveAllele(EnumBeeChromosome.LIFESPAN.ordinal()).getName(),
-				bee.getGenome().getInactiveAllele(EnumBeeChromosome.LIFESPAN.ordinal()).getName(), bee,
+		drawRow(StringUtil.localize("gui.lifespan"), bee.getGenome().getActiveAllele(EnumBeeChromosome.LIFESPAN).getName(),
+				bee.getGenome().getInactiveAllele(EnumBeeChromosome.LIFESPAN).getName(), bee,
 				EnumBeeChromosome.LIFESPAN);
 
-		drawRow(StringUtil.localize("gui.speed"), bee.getGenome().getActiveAllele(EnumBeeChromosome.SPEED.ordinal()).getName(),
-				bee.getGenome().getInactiveAllele(EnumBeeChromosome.SPEED.ordinal()).getName(), bee, EnumBeeChromosome.SPEED);
+		drawRow(StringUtil.localize("gui.speed"), bee.getGenome().getActiveAllele(EnumBeeChromosome.SPEED).getName(),
+				bee.getGenome().getInactiveAllele(EnumBeeChromosome.SPEED).getName(), bee, EnumBeeChromosome.SPEED);
 
-		drawRow(StringUtil.localize("gui.pollination"), bee.getGenome().getActiveAllele(EnumBeeChromosome.FLOWERING.ordinal()).getName(),
-				bee.getGenome().getInactiveAllele(EnumBeeChromosome.FLOWERING.ordinal()).getName(), bee,
+		drawRow(StringUtil.localize("gui.pollination"), bee.getGenome().getActiveAllele(EnumBeeChromosome.FLOWERING).getName(),
+				bee.getGenome().getInactiveAllele(EnumBeeChromosome.FLOWERING).getName(), bee,
 				EnumBeeChromosome.FLOWERING);
 
 		drawRow(StringUtil.localize("gui.flowers"), bee.getGenome().getFlowerProvider().getDescription(),
-				((IAlleleFlowers) bee.getGenome().getInactiveAllele(EnumBeeChromosome.FLOWER_PROVIDER.ordinal())).getProvider()
+				((IAlleleFlowers) bee.getGenome().getInactiveAllele(EnumBeeChromosome.FLOWER_PROVIDER)).getProvider()
 						.getDescription(), bee, EnumBeeChromosome.FLOWER_PROVIDER);
 
 		drawLine(StringUtil.localize("gui.fertility"), COLUMN_0);
-		drawFertilityInfo(bee.getGenome().getFertility(), COLUMN_1, getColorCoding(bee.getGenome().getActiveAllele(EnumBeeChromosome.FERTILITY.ordinal())
+		drawFertilityInfo(bee.getGenome().getFertility(), COLUMN_1, getColorCoding(bee.getGenome().getActiveAllele(EnumBeeChromosome.FERTILITY)
 				.isDominant()), 0);
-		drawFertilityInfo(((IAlleleInteger) bee.getGenome().getInactiveAllele(EnumBeeChromosome.FERTILITY.ordinal())).getValue(), COLUMN_2, getColorCoding(bee
-				.getGenome().getInactiveAllele(EnumBeeChromosome.FERTILITY.ordinal()).isDominant()), 0);
+		drawFertilityInfo(((IAlleleInteger) bee.getGenome().getInactiveAllele(EnumBeeChromosome.FERTILITY)).getValue(), COLUMN_2, getColorCoding(bee
+				.getGenome().getInactiveAllele(EnumBeeChromosome.FERTILITY).isDominant()), 0);
 
 		newLine();
 
 		int[] areaAr = bee.getGenome().getTerritory();
 		Vect area = new Vect(areaAr[0], areaAr[1], areaAr[2]);
-		drawRow(StringUtil.localize("gui.area"), area.toString(), ((AlleleArea) bee.getGenome().getInactiveAllele(EnumBeeChromosome.TERRITORY.ordinal()))
+		drawRow(StringUtil.localize("gui.area"), area.toString(), ((AlleleArea) bee.getGenome().getInactiveAllele(EnumBeeChromosome.TERRITORY))
 				.getArea().toString(), bee, EnumBeeChromosome.TERRITORY);
 
 		drawRow(StringUtil.localize("gui.effect"), bee.getGenome().getEffect().getName(),
-				bee.getGenome().getInactiveAllele(EnumBeeChromosome.EFFECT.ordinal()).getName(), bee,
+				bee.getGenome().getInactiveAllele(EnumBeeChromosome.EFFECT).getName(), bee,
 				EnumBeeChromosome.EFFECT);
 
 		newLine();
@@ -161,8 +155,8 @@ public class GuiBeealyzer extends GuiAlyzer {
 		drawRow(StringUtil.localize("gui.climate"), AlleleManager.climateHelper.toDisplay(bee.getGenome().getPrimary().getTemperature()),
 				AlleleManager.climateHelper.toDisplay(bee.getGenome().getSecondary().getTemperature()), bee, EnumBeeChromosome.SPECIES);
 
-		IAlleleTolerance tempToleranceActive = (IAlleleTolerance)bee.getGenome().getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE.ordinal());
-		IAlleleTolerance tempToleranceInactive = (IAlleleTolerance)bee.getGenome().getInactiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE.ordinal());
+		IAlleleTolerance tempToleranceActive = (IAlleleTolerance)bee.getGenome().getActiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE);
+		IAlleleTolerance tempToleranceInactive = (IAlleleTolerance)bee.getGenome().getInactiveAllele(EnumBeeChromosome.TEMPERATURE_TOLERANCE);
 		drawLine(StringUtil.localize("gui.temptol"), COLUMN_0);
 		drawToleranceInfo(tempToleranceActive, COLUMN_1);
 		drawToleranceInfo(tempToleranceInactive, COLUMN_2);
@@ -172,8 +166,8 @@ public class GuiBeealyzer extends GuiAlyzer {
 		drawRow(StringUtil.localize("gui.humidity"), AlleleManager.climateHelper.toDisplay(bee.getGenome().getPrimary().getHumidity()),
 				AlleleManager.climateHelper.toDisplay(bee.getGenome().getSecondary().getHumidity()), bee, EnumBeeChromosome.SPECIES);
 
-		IAlleleTolerance humidToleranceActive = (IAlleleTolerance)bee.getGenome().getActiveAllele(EnumBeeChromosome.HUMIDITY_TOLERANCE.ordinal());
-		IAlleleTolerance humidToleranceInactive = (IAlleleTolerance)bee.getGenome().getInactiveAllele(EnumBeeChromosome.HUMIDITY_TOLERANCE.ordinal());
+		IAlleleTolerance humidToleranceActive = (IAlleleTolerance)bee.getGenome().getActiveAllele(EnumBeeChromosome.HUMIDITY_TOLERANCE);
+		IAlleleTolerance humidToleranceInactive = (IAlleleTolerance)bee.getGenome().getInactiveAllele(EnumBeeChromosome.HUMIDITY_TOLERANCE);
 		drawLine(StringUtil.localize("gui.humidtol"), COLUMN_0);
 		drawToleranceInfo(humidToleranceActive, COLUMN_1);
 		drawToleranceInfo(humidToleranceInactive, COLUMN_2);
@@ -191,7 +185,7 @@ public class GuiBeealyzer extends GuiAlyzer {
 			nocturnal0 = bee.getGenome().getPrimary().isNocturnal() ? yes : no;
 			diurnal0 = !bee.getGenome().getPrimary().isNocturnal() ? yes : no;
 		}
-		if(((AlleleBoolean) bee.getGenome().getInactiveAllele(EnumBeeChromosome.NOCTURNAL.ordinal())).getValue()) {
+		if(((AlleleBoolean) bee.getGenome().getInactiveAllele(EnumBeeChromosome.NOCTURNAL)).getValue()) {
 			nocturnal1 = diurnal1 = yes;
 		} else {
 			nocturnal1 = bee.getGenome().getSecondary().isNocturnal() ? yes : no;
@@ -209,13 +203,13 @@ public class GuiBeealyzer extends GuiAlyzer {
 		newLine();
 
 		String primary = StringUtil.readableBoolean(bee.getGenome().getTolerantFlyer(), yes, no);
-		String secondary = StringUtil.readableBoolean(((AlleleBoolean) bee.getGenome().getInactiveAllele(EnumBeeChromosome.TOLERANT_FLYER.ordinal())).getValue(), yes,
+		String secondary = StringUtil.readableBoolean(((AlleleBoolean) bee.getGenome().getInactiveAllele(EnumBeeChromosome.TOLERANT_FLYER)).getValue(), yes,
 				no);
 
 		drawRow(StringUtil.localize("gui.flyer"), primary, secondary, bee, EnumBeeChromosome.TOLERANT_FLYER);
 
 		primary = StringUtil.readableBoolean(bee.getGenome().getCaveDwelling(), yes, no);
-		secondary = StringUtil.readableBoolean(((AlleleBoolean) bee.getGenome().getInactiveAllele(EnumBeeChromosome.CAVE_DWELLING.ordinal())).getValue(), yes,
+		secondary = StringUtil.readableBoolean(((AlleleBoolean) bee.getGenome().getInactiveAllele(EnumBeeChromosome.CAVE_DWELLING)).getValue(), yes,
 				no);
 
 		drawRow(StringUtil.localize("gui.cave"), primary, secondary, bee, EnumBeeChromosome.CAVE_DWELLING);
@@ -246,8 +240,6 @@ public class GuiBeealyzer extends GuiAlyzer {
 		float factor = this.factor;
 		this.setFactor(1.0f);
 
-		tempProductList = bee.getProduceList();
-
 		startPage(COLUMN_0, COLUMN_1, COLUMN_2);
 
 		drawLine(StringUtil.localize("gui.beealyzer.produce") + ":", COLUMN_0);
@@ -255,7 +247,7 @@ public class GuiBeealyzer extends GuiAlyzer {
 		newLine();
 
 		int x = COLUMN_0;
-		for (ItemStack stack : tempProductList) {
+		for (ItemStack stack : bee.getProduceList()) {
 			widgetManager.add(new ItemStackWidget(adjustToFactor(x), adjustToFactor(getLineY()), stack));
 
 			x += 18;

src/main/java/forestry/arboriculture/FruitProviderPod.java

@@ -82,7 +82,7 @@ public class FruitProviderPod extends FruitProviderNone {
 		if (type == EnumPodType.COCOA)
 			return BlockUtil.tryPlantPot(world, x, y, z, Blocks.cocoa);
 		else {
-			return PluginArboriculture.treeInterface.setFruitBlock(world, (IAlleleFruit) genome.getActiveAllele(EnumTreeChromosome.FRUITS.ordinal()),
+			return PluginArboriculture.treeInterface.setFruitBlock(world, (IAlleleFruit) genome.getActiveAllele(EnumTreeChromosome.FRUITS),
 					genome.getSappiness(), type.uids, x, y, z);
 		}
 	}

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

@@ -144,7 +144,7 @@ public class AlleleTreeSpecies extends AlleleSpecies implements IAlleleTreeSpeci
 		int highest = 0;
 		exclude.add(species);
 
-		for(IMutation mutation : getRoot().getPaths(species, EnumBeeChromosome.SPECIES.ordinal())) {
+		for(IMutation mutation : getRoot().getPaths(species, EnumBeeChromosome.SPECIES)) {
 			if(!exclude.contains(mutation.getAllele0())) {
 				int otherAdvance = getGeneticAdvancement(mutation.getAllele0(), exclude);
 				if(otherAdvance > highest)

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

@@ -108,7 +108,7 @@ public class Tree extends Individual implements ITree, ITreeGenData, IPlantable
 	/* EFFECTS */
 	@Override
 	public IEffectData[] doEffect(IEffectData[] storedData, World world, int biomeid, int x, int y, int z) {
-		IAlleleLeafEffect effect = (IAlleleLeafEffect) getGenome().getActiveAllele(EnumTreeChromosome.EFFECT.ordinal());
+		IAlleleLeafEffect effect = (IAlleleLeafEffect) getGenome().getActiveAllele(EnumTreeChromosome.EFFECT);
 
 		if (effect == null)
 			return null;
@@ -119,7 +119,7 @@ public class Tree extends Individual implements ITree, ITreeGenData, IPlantable
 		if (!effect.isCombinable())
 			return storedData;
 
-		IAlleleLeafEffect secondary = (IAlleleLeafEffect) getGenome().getInactiveAllele(EnumTreeChromosome.EFFECT.ordinal());
+		IAlleleLeafEffect secondary = (IAlleleLeafEffect) getGenome().getInactiveAllele(EnumTreeChromosome.EFFECT);
 		if (!secondary.isCombinable())
 			return storedData;
 
@@ -255,7 +255,7 @@ public class Tree extends Individual implements ITree, ITreeGenData, IPlantable
 
 	@Override
 	public boolean isPureBred(EnumTreeChromosome chromosome) {
-		return genome.getActiveAllele(chromosome.ordinal()).getUID().equals(genome.getInactiveAllele(chromosome.ordinal()).getUID());
+		return genome.getActiveAllele(chromosome).getUID().equals(genome.getInactiveAllele(chromosome).getUID());
 	}
 
 	@Override
@@ -279,16 +279,16 @@ public class Tree extends Individual implements ITree, ITreeGenData, IPlantable
 		IAlleleTreeSpecies secondary = genome.getSecondary();
 		if (!isPureBred(EnumTreeChromosome.SPECIES))
 			list.add("\u00A79" + StringUtil.localize("trees.hybrid").replaceAll("%PRIMARY",primary.getName()).replaceAll("%SECONDARY",secondary.getName()));
-		list.add(String.format("\u00A76S: %s, \u00A7cM: %s", genome.getActiveAllele(EnumTreeChromosome.SAPPINESS.ordinal()).getName(), genome.getActiveAllele(EnumTreeChromosome.MATURATION.ordinal()).getName()));
-		list.add(String.format("\u00A7dH: %s, \u00A7bG: %sx%s", genome.getActiveAllele(EnumTreeChromosome.HEIGHT.ordinal()).getName(), genome.getGirth(), genome.getGirth()));
+		list.add(String.format("\u00A76S: %s, \u00A7cM: %s", genome.getActiveAllele(EnumTreeChromosome.SAPPINESS).getName(), genome.getActiveAllele(EnumTreeChromosome.MATURATION).getName()));
+		list.add(String.format("\u00A7dH: %s, \u00A7bG: %sx%s", genome.getActiveAllele(EnumTreeChromosome.HEIGHT).getName(), genome.getGirth(), genome.getGirth()));
 
-		list.add(String.format("\u00A7eS: %s, \u00A7fY: %s", genome.getActiveAllele(EnumTreeChromosome.FERTILITY.ordinal()).getName(), genome.getActiveAllele(EnumTreeChromosome.YIELD.ordinal()).getName()));
+		list.add(String.format("\u00A7eS: %s, \u00A7fY: %s", genome.getActiveAllele(EnumTreeChromosome.FERTILITY).getName(), genome.getActiveAllele(EnumTreeChromosome.YIELD).getName()));
 
-		IAlleleBoolean primaryFireproof = (IAlleleBoolean)genome.getActiveAllele(EnumTreeChromosome.FIREPROOF.ordinal());
+		IAlleleBoolean primaryFireproof = (IAlleleBoolean)genome.getActiveAllele(EnumTreeChromosome.FIREPROOF);
 		if (primaryFireproof.getValue())
 			list.add(String.format("\u00A7c%s", StatCollector.translateToLocal("for.gui.fireresist")));
 
-		IAllele fruit = getGenome().getActiveAllele(EnumTreeChromosome.FRUITS.ordinal());
+		IAllele fruit = getGenome().getActiveAllele(EnumTreeChromosome.FRUITS);
 		if(fruit != Allele.fruitNone) {
 			String strike = "";
 			if (!canBearFruit())

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

@@ -57,37 +57,37 @@ public class TreeGenome extends Genome implements ITreeGenome {
 
 	@Override
 	public IAlleleTreeSpecies getPrimary() {
-		return (IAlleleTreeSpecies) getActiveAllele(EnumTreeChromosome.SPECIES.ordinal());
+		return (IAlleleTreeSpecies) getActiveAllele(EnumTreeChromosome.SPECIES);
 	}
 
 	@Override
 	public IAlleleTreeSpecies getSecondary() {
-		return (IAlleleTreeSpecies) getInactiveAllele(EnumTreeChromosome.SPECIES.ordinal());
+		return (IAlleleTreeSpecies) getInactiveAllele(EnumTreeChromosome.SPECIES);
 	}
 
 	@Override
 	public IFruitProvider getFruitProvider() {
-		return ((IAlleleFruit) getActiveAllele(EnumTreeChromosome.FRUITS.ordinal())).getProvider();
+		return ((IAlleleFruit) getActiveAllele(EnumTreeChromosome.FRUITS)).getProvider();
 	}
 
 	@Override
 	public IGrowthProvider getGrowthProvider() {
-		return ((IAlleleGrowth) getActiveAllele(EnumTreeChromosome.GROWTH.ordinal())).getProvider();
+		return ((IAlleleGrowth) getActiveAllele(EnumTreeChromosome.GROWTH)).getProvider();
 	}
 
 	@Override
 	public float getHeight() {
-		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.HEIGHT.ordinal())).getValue();
+		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.HEIGHT)).getValue();
 	}
 
 	@Override
 	public float getFertility() {
-		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.FERTILITY.ordinal())).getValue();
+		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.FERTILITY)).getValue();
 	}
 
 	@Override
 	public float getYield() {
-		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.YIELD.ordinal())).getValue();
+		return ((IAlleleFloat) getActiveAllele(EnumTreeChromosome.YIELD)).getValue();
 	}
 
 	@Override
@@ -96,7 +96,7 @@ public class TreeGenome extends Genome implements ITreeGenome {
 		if (getChromosomes()[EnumTreeChromosome.SAPPINESS.ordinal()] == null)
 			getChromosomes()[EnumTreeChromosome.SAPPINESS.ordinal()] = new Chromosome(Allele.sappinessLowest);
 
-		IAllele allele = getActiveAllele(EnumTreeChromosome.SAPPINESS.ordinal());
+		IAllele allele = getActiveAllele(EnumTreeChromosome.SAPPINESS);
 		// FIXME: More legacy handling
 		if (allele instanceof IAlleleFloat)
 			return ((IAlleleFloat) allele).getValue();
@@ -109,10 +109,10 @@ public class TreeGenome extends Genome implements ITreeGenome {
 	@Override
 	public EnumSet<EnumPlantType> getPlantTypes() {
 		// / FIXME: Needs some legacy handling.
-		if (!(getActiveAllele(EnumTreeChromosome.PLANT.ordinal()) instanceof AllelePlantType))
+		if (!(getActiveAllele(EnumTreeChromosome.PLANT) instanceof AllelePlantType))
 			getChromosomes()[EnumTreeChromosome.PLANT.ordinal()] = new Chromosome(Allele.plantTypeNone);
 
-		return ((AllelePlantType) getActiveAllele(EnumTreeChromosome.PLANT.ordinal())).getPlantTypes();
+		return ((AllelePlantType) getActiveAllele(EnumTreeChromosome.PLANT)).getPlantTypes();
 	}
 
 	@Override
@@ -120,7 +120,7 @@ public class TreeGenome extends Genome implements ITreeGenome {
 		if (getChromosomes()[EnumTreeChromosome.MATURATION.ordinal()] == null)
 			getChromosomes()[EnumTreeChromosome.MATURATION.ordinal()] = new Chromosome(Allele.maturationSlowest);
 
-		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.MATURATION.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.MATURATION)).getValue();
 	}
 
 	private IAllele translateGirth(int girth) {
@@ -136,12 +136,12 @@ public class TreeGenome extends Genome implements ITreeGenome {
 
 	@Override
 	public int getGirth() {
-		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.GIRTH.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumTreeChromosome.GIRTH)).getValue();
 	}
 	
 	@Override
 	public IAlleleLeafEffect getEffect() {
-		return (IAlleleLeafEffect) getActiveAllele(EnumTreeChromosome.EFFECT.ordinal());
+		return (IAlleleLeafEffect) getActiveAllele(EnumTreeChromosome.EFFECT);
 	}
 
 	@Override

src/main/java/forestry/arboriculture/gui/GuiTreealyzer.java

@@ -42,10 +42,7 @@ import java.util.Locale;
 public class GuiTreealyzer extends GuiAlyzer {
 
 	public GuiTreealyzer(EntityPlayer player, TreealyzerInventory inventory) {
-		super(AlleleManager.alleleRegistry.getSpeciesRoot("rootTrees"), player,
-				new ContainerTreealyzer(player.inventory, inventory), inventory, 1, inventory.getSizeInventory());
-
-		guiName = "gui.treealyzer";
+		super("rootTrees", player, new ContainerTreealyzer(player.inventory, inventory), inventory, "gui.treealyzer");
 
 		ArrayList<ItemStack> treeList = new ArrayList<ItemStack>();
 		((ItemGermlingGE) ForestryItem.sapling.item()).addCreativeItems(treeList, false);
@@ -127,42 +124,42 @@ public class GuiTreealyzer extends GuiAlyzer {
 		newLine();
 
 		drawLine(StringUtil.localize("gui.saplings"), COLUMN_0);
-		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.FERTILITY.ordinal()).getName(), COLUMN_1, tree, EnumTreeChromosome.FERTILITY, false);
-		drawLine(tree.getGenome().getInactiveAllele(EnumTreeChromosome.FERTILITY.ordinal()).getName(), COLUMN_2, tree,
+		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.FERTILITY).getName(), COLUMN_1, tree, EnumTreeChromosome.FERTILITY, false);
+		drawLine(tree.getGenome().getInactiveAllele(EnumTreeChromosome.FERTILITY).getName(), COLUMN_2, tree,
 				EnumTreeChromosome.FERTILITY, true);
 
 		newLine();
 
-		drawRow(StringUtil.localize("gui.maturity"), tree.getGenome().getActiveAllele(EnumTreeChromosome.MATURATION.ordinal()).getName(),
-				tree.getGenome().getInactiveAllele(EnumTreeChromosome.MATURATION.ordinal()).getName(), tree,
+		drawRow(StringUtil.localize("gui.maturity"), tree.getGenome().getActiveAllele(EnumTreeChromosome.MATURATION).getName(),
+				tree.getGenome().getInactiveAllele(EnumTreeChromosome.MATURATION).getName(), tree,
 				EnumTreeChromosome.MATURATION);
 
 		drawLine(StringUtil.localize("gui.height"), COLUMN_0);
-		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.HEIGHT.ordinal()).getName(), COLUMN_1, tree, EnumTreeChromosome.HEIGHT, false);
-		drawLine(tree.getGenome().getInactiveAllele(EnumTreeChromosome.HEIGHT.ordinal()).getName(), COLUMN_2, tree,
+		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.HEIGHT).getName(), COLUMN_1, tree, EnumTreeChromosome.HEIGHT, false);
+		drawLine(tree.getGenome().getInactiveAllele(EnumTreeChromosome.HEIGHT).getName(), COLUMN_2, tree,
 				EnumTreeChromosome.HEIGHT, true);
 
 		newLine();
 
 		drawLine(StringUtil.localize("gui.girth"), COLUMN_0);
 		drawLine(String.format("%sx%s", tree.getGenome().getGirth(), tree.getGenome().getGirth()), COLUMN_1, tree, EnumTreeChromosome.FERTILITY, false);
-		int secondGirth = ((IAlleleInteger) tree.getGenome().getInactiveAllele(EnumTreeChromosome.GIRTH.ordinal())).getValue();
+		int secondGirth = ((IAlleleInteger) tree.getGenome().getInactiveAllele(EnumTreeChromosome.GIRTH)).getValue();
 		drawLine(String.format("%sx%s", secondGirth, secondGirth), COLUMN_2, tree, EnumTreeChromosome.FERTILITY, true);
 
 		newLine();
 
 		drawLine(StringUtil.localize("gui.yield"), COLUMN_0);
-		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.YIELD.ordinal()).getName(), COLUMN_1, tree, EnumTreeChromosome.YIELD, false);
-		drawLine(tree.getGenome().getInactiveAllele(EnumTreeChromosome.YIELD.ordinal()).getName(), COLUMN_2, tree,
+		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.YIELD).getName(), COLUMN_1, tree, EnumTreeChromosome.YIELD, false);
+		drawLine(tree.getGenome().getInactiveAllele(EnumTreeChromosome.YIELD).getName(), COLUMN_2, tree,
 				EnumTreeChromosome.YIELD, true);
 
 		newLine();
 
 		drawLine(StringUtil.localize("gui.sappiness"), COLUMN_0);
-		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.SAPPINESS.ordinal()).getName(), COLUMN_1, tree, EnumTreeChromosome.SAPPINESS, false);
+		drawLine(tree.getGenome().getActiveAllele(EnumTreeChromosome.SAPPINESS).getName(), COLUMN_1, tree, EnumTreeChromosome.SAPPINESS, false);
 
 		// FIXME: Legacy handling
-		IAllele sappiness = tree.getGenome().getInactiveAllele(EnumTreeChromosome.SAPPINESS.ordinal());
+		IAllele sappiness = tree.getGenome().getInactiveAllele(EnumTreeChromosome.SAPPINESS);
 		String sap;
 		if (sappiness instanceof IAlleleFloat)
 			sap = sappiness.getName();
@@ -176,8 +173,8 @@ public class GuiTreealyzer extends GuiAlyzer {
 		String yes = StringUtil.localize("yes");
 		String no = StringUtil.localize("no");
 
-		AlleleBoolean primaryFireproof = (AlleleBoolean)tree.getGenome().getActiveAllele(EnumTreeChromosome.FIREPROOF.ordinal());
-		AlleleBoolean secondaryFireproof = (AlleleBoolean)tree.getGenome().getInactiveAllele(EnumTreeChromosome.FIREPROOF.ordinal());
+		AlleleBoolean primaryFireproof = (AlleleBoolean)tree.getGenome().getActiveAllele(EnumTreeChromosome.FIREPROOF);
+		AlleleBoolean secondaryFireproof = (AlleleBoolean)tree.getGenome().getInactiveAllele(EnumTreeChromosome.FIREPROOF);
 
 		drawLine(StringUtil.localize("gui.fireproof"), COLUMN_0);
 		drawLine(StringUtil.readableBoolean(primaryFireproof.getValue(), yes, no), COLUMN_1, tree, EnumTreeChromosome.FIREPROOF, false);
@@ -186,7 +183,7 @@ public class GuiTreealyzer extends GuiAlyzer {
 		newLine();
 
 		drawRow(StringUtil.localize("gui.effect"), tree.getGenome().getEffect().getName(),
-				tree.getGenome().getInactiveAllele(EnumTreeChromosome.EFFECT.ordinal()).getName(), tree,
+				tree.getGenome().getInactiveAllele(EnumTreeChromosome.EFFECT).getName(), tree,
 				EnumTreeChromosome.EFFECT);
 
 		newLine();
@@ -210,7 +207,7 @@ public class GuiTreealyzer extends GuiAlyzer {
 
 		drawLine(StringUtil.localize("gui.growth"), COLUMN_0);
 		drawLine(tree.getGenome().getGrowthProvider().getDescription(), COLUMN_1, tree, EnumTreeChromosome.GROWTH, false);
-		drawLine(((IAlleleGrowth) tree.getGenome().getInactiveAllele(EnumTreeChromosome.GROWTH.ordinal())).getProvider().getDescription(), COLUMN_2, tree,
+		drawLine(((IAlleleGrowth) tree.getGenome().getInactiveAllele(EnumTreeChromosome.GROWTH)).getProvider().getDescription(), COLUMN_2, tree,
 				EnumTreeChromosome.GROWTH, true);
 
 		newLine();
@@ -228,7 +225,7 @@ public class GuiTreealyzer extends GuiAlyzer {
 		List<EnumPlantType> tolerated0 = new ArrayList<EnumPlantType>(tree.getGenome().getPlantTypes());
 		List<EnumPlantType> tolerated1 = Collections.emptyList();
 
-		IAllele allele1 = tree.getGenome().getInactiveAllele(EnumTreeChromosome.PLANT.ordinal());
+		IAllele allele1 = tree.getGenome().getInactiveAllele(EnumTreeChromosome.PLANT);
 		if (allele1 instanceof AllelePlantType) {
 			tolerated1 = new ArrayList<EnumPlantType>(((AllelePlantType) allele1).getPlantTypes());
 		}
@@ -264,18 +261,18 @@ public class GuiTreealyzer extends GuiAlyzer {
 		newLine();
 		newLine();
 
-		int fruitDominance0 = getColorCoding(tree.getGenome().getActiveAllele(EnumTreeChromosome.FRUITS.ordinal()).isDominant());
-		int fruitDominance1 = getColorCoding(tree.getGenome().getInactiveAllele(EnumTreeChromosome.FRUITS.ordinal()).isDominant());
+		int fruitDominance0 = getColorCoding(tree.getGenome().getActiveAllele(EnumTreeChromosome.FRUITS).isDominant());
+		int fruitDominance1 = getColorCoding(tree.getGenome().getInactiveAllele(EnumTreeChromosome.FRUITS).isDominant());
 
 		drawLine(StringUtil.localize("gui.fruits"), COLUMN_0);
 		String strike = "";
-		IAllele fruit0 = tree.getGenome().getActiveAllele(EnumTreeChromosome.FRUITS.ordinal());
+		IAllele fruit0 = tree.getGenome().getActiveAllele(EnumTreeChromosome.FRUITS);
 		if (!tree.canBearFruit() && fruit0 != Allele.fruitNone)
 			strike = "\u00A7m";
 		drawLine(strike + StringUtil.localize(tree.getGenome().getFruitProvider().getDescription()), COLUMN_1, fruitDominance0);
 
 		strike = "";
-		IAllele fruit1 = tree.getGenome().getInactiveAllele(EnumTreeChromosome.FRUITS.ordinal());
+		IAllele fruit1 = tree.getGenome().getInactiveAllele(EnumTreeChromosome.FRUITS);
 		if (!tree.getGenome().getSecondary().getSuitableFruit().contains(((IAlleleFruit) fruit1).getProvider().getFamily()) && fruit1 != Allele.fruitNone)
 			strike = "\u00A7m";
 		drawLine(strike + StringUtil.localize(((IAlleleFruit) fruit1).getProvider().getDescription()), COLUMN_2, fruitDominance1);
@@ -284,7 +281,7 @@ public class GuiTreealyzer extends GuiAlyzer {
 
 		drawLine(StringUtil.localize("gui.family"), COLUMN_0);
 		IFruitFamily primary = tree.getGenome().getFruitProvider().getFamily();
-		IFruitFamily secondary = ((IAlleleFruit) tree.getGenome().getInactiveAllele(EnumTreeChromosome.FRUITS.ordinal())).getProvider().getFamily();
+		IFruitFamily secondary = ((IAlleleFruit) tree.getGenome().getInactiveAllele(EnumTreeChromosome.FRUITS)).getProvider().getFamily();
 
 		if (primary != null)
 			drawLine(primary.getName(), COLUMN_1, fruitDominance0);

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

@@ -109,7 +109,7 @@ public abstract class WorldGenTree extends WorldGenArboriculture {
 
 		// if we have a fireproof tree, return the fireproof log
 		if (block instanceof BlockLog) {
-			IAlleleBoolean fireproof = (IAlleleBoolean) tree.getGenome().getActiveAllele(EnumTreeChromosome.FIREPROOF.ordinal());
+			IAlleleBoolean fireproof = (IAlleleBoolean) tree.getGenome().getActiveAllele(EnumTreeChromosome.FIREPROOF);
 			if (fireproof.getValue()) {
 				BlockLog blockLog = (BlockLog) block;
 				ForestryBlock fireproofLogBlock = BlockFireproofLog.getFireproofLog(blockLog);

src/main/java/forestry/core/gadgets/BlockStainedGlass.java

@@ -101,4 +101,9 @@ public class BlockStainedGlass extends BlockBreakable {
 		return false;
 	}
 
+	@Override
+	protected boolean canSilkHarvest() {
+		return true;
+	}
+
 }

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

@@ -118,8 +118,8 @@ public class Allele implements IAllele {
 
 	// Agrarian branch
 	public static AlleleSpecies speciesRural;
-	// 41 Farmerly
-	// 42 Agrarian
+	public static AlleleSpecies speciesFarmerly;
+	public static AlleleSpecies speciesArgrarian;
 
 	// Boggy branch
 	public static AlleleSpecies speciesMarshy;
@@ -391,6 +391,7 @@ public class Allele implements IAllele {
 	public static Allele effectReanimation;
 	public static Allele effectResurrection;
 	public static Allele effectRepulsion;
+	public static Allele effectFertile;
 
 	// / TREES // EFFECTS
 	public static Allele leavesNone;

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

@@ -16,7 +16,6 @@ import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IChromosome;
 import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IGenome;
-import forestry.apiculture.items.ItemBeeGE;
 import forestry.core.config.Config;
 import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
@@ -136,11 +135,21 @@ public abstract class Genome implements IGenome {
 		return chromosomes[chromosome].getActiveAllele();
 	}
 
+	@Override
+	public IAllele getActiveAllele(IChromosomeType chromosomeType) {
+		return chromosomes[chromosomeType.ordinal()].getActiveAllele();
+	}
+
 	@Override
 	public IAllele getInactiveAllele(int chromosome) {
 		return chromosomes[chromosome].getInactiveAllele();
 	}
 
+	@Override
+	public IAllele getInactiveAllele(IChromosomeType chromosomeType) {
+		return chromosomes[chromosomeType.ordinal()].getInactiveAllele();
+	}
+
 	@Override
 	public boolean isGeneticEqual(IGenome other) {
 		IChromosome[] genetics = other.getChromosomes();

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

@@ -10,6 +10,7 @@
  ******************************************************************************/
 package forestry.core.genetics;
 
+import forestry.api.genetics.IChromosomeType;
 import net.minecraft.nbt.NBTTagCompound;
 
 import forestry.api.genetics.IIndividual;
@@ -74,8 +75,13 @@ public abstract class Individual implements IIndividual {
 	}
 
 	@Override
+	@SuppressWarnings("deprecated")
 	public boolean isPureBred(int chromosomeOrdinal) {
 		return getGenome().getActiveAllele(chromosomeOrdinal).getUID().equals(getGenome().getInactiveAllele(chromosomeOrdinal).getUID());
 	}
 
+	@Override
+	public boolean isPureBred(IChromosomeType chromosomeType) {
+		return getGenome().getActiveAllele(chromosomeType).getUID().equals(getGenome().getInactiveAllele(chromosomeType).getUID());
+	}
 }

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

@@ -10,6 +10,13 @@
  ******************************************************************************/
 package forestry.core.genetics;
 
+import forestry.api.genetics.IAllele;
+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;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -18,13 +25,6 @@ import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Random;
 
-import net.minecraft.item.ItemStack;
-
-import forestry.api.genetics.IAllele;
-import forestry.api.genetics.IChromosome;
-import forestry.api.genetics.IMutation;
-import forestry.api.genetics.ISpeciesRoot;
-
 public abstract class SpeciesRoot implements ISpeciesRoot {
 	
 	/* RESEARCH */
@@ -74,6 +74,7 @@ public abstract class SpeciesRoot implements ISpeciesRoot {
 		return combinations;
 	}
 
+	@Deprecated
 	@Override
 	public Collection<? extends IMutation> getPaths(IAllele result, int chromosomeOrdinal) {
 		ArrayList<IMutation> paths = new ArrayList<IMutation>();
@@ -84,6 +85,16 @@ public abstract class SpeciesRoot implements ISpeciesRoot {
 		return paths;
 	}
 
+	@Override
+	public Collection<? extends IMutation> getPaths(IAllele result, IChromosomeType chromosomeType) {
+		ArrayList<IMutation> paths = new ArrayList<IMutation>();
+		for (IMutation mutation : getMutations(false))
+			if(mutation.getTemplate()[chromosomeType.ordinal()] == result)
+				paths.add(mutation);
+
+		return paths;
+	}
+
 	/* GENOME CONVERSIONS */
 	@Override
 	public IChromosome[] templateAsChromosomes(IAllele[] template) {

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

@@ -17,6 +17,7 @@ import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IAlleleTolerance;
 import forestry.api.genetics.IBreedingTracker;
+import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IClassification;
 import forestry.api.genetics.IClassification.EnumClassLevel;
 import forestry.api.genetics.IIndividual;
@@ -49,19 +50,21 @@ public abstract class GuiAlyzer extends GuiForestry<TileForestry> {
 	protected ISpeciesRoot speciesRoot;
 	protected IBreedingTracker breedingTracker;
 
-	protected String guiName;
+	protected final String guiName;
 
 	protected HashMap<String, ItemStack> iconStacks = new HashMap<String, ItemStack>();
 
-	public GuiAlyzer(ISpeciesRoot speciesRoot, EntityPlayer player, ContainerForestry container, IInventory inventory, int pageMax, int pageSize) {
+	public GuiAlyzer(String speciesRoot, EntityPlayer player, ContainerForestry container, IInventory inventory, String guiName) {
 		super(Defaults.TEXTURE_PATH_GUI + "/beealyzer2.png", container);
 
-		xSize = 246;
-		ySize = 238;
+		this.xSize = 246;
+		this.ySize = 238;
+
+		this.guiName = guiName;
 
 		this.inventory = inventory;
-		this.speciesRoot = speciesRoot;
-		this.breedingTracker = speciesRoot.getBreedingTracker(player.worldObj, player.getGameProfile());
+		this.speciesRoot = AlleleManager.alleleRegistry.getSpeciesRoot(speciesRoot);
+		this.breedingTracker = this.speciesRoot.getBreedingTracker(player.worldObj, player.getGameProfile());
 	}
 
 	protected final int getColorCoding(boolean dominant) {
@@ -71,26 +74,26 @@ public abstract class GuiAlyzer extends GuiForestry<TileForestry> {
 			return fontColor.get("gui.beealyzer.recessive");
 	}
 
-	protected final void drawLine(String text, int x, IIndividual individual, Enum<?> chromosome, boolean inactive) {
+	protected final void drawLine(String text, int x, IIndividual individual, IChromosomeType chromosome, boolean inactive) {
 		if (!inactive)
-			drawLine(text, x, getColorCoding(individual.getGenome().getActiveAllele(chromosome.ordinal()).isDominant()));
+			drawLine(text, x, getColorCoding(individual.getGenome().getActiveAllele(chromosome).isDominant()));
 		else
-			drawLine(text, x, getColorCoding(individual.getGenome().getInactiveAllele(chromosome.ordinal()).isDominant()));
+			drawLine(text, x, getColorCoding(individual.getGenome().getInactiveAllele(chromosome).isDominant()));
 	}
 
-	protected final void drawSplitLine(String text, int x, int maxWidth, IIndividual individual, Enum<?> chromosome, boolean inactive) {
+	protected final void drawSplitLine(String text, int x, int maxWidth, IIndividual individual, IChromosomeType chromosome, boolean inactive) {
 		if (!inactive)
-			drawSplitLine(text, x, maxWidth, getColorCoding(individual.getGenome().getActiveAllele(chromosome.ordinal()).isDominant()));
+			drawSplitLine(text, x, maxWidth, getColorCoding(individual.getGenome().getActiveAllele(chromosome).isDominant()));
 		else
-			drawSplitLine(text, x, maxWidth, getColorCoding(individual.getGenome().getInactiveAllele(chromosome.ordinal()).isDominant()));
+			drawSplitLine(text, x, maxWidth, getColorCoding(individual.getGenome().getInactiveAllele(chromosome).isDominant()));
 	}
 
-	protected final void drawRow(String text0, String text1, String text2, IIndividual individual, Enum<?> chromosome) {
-		drawRow(text0, text1, text2, fontColor.get("gui.screen"), getColorCoding(individual.getGenome().getActiveAllele(chromosome.ordinal()).isDominant()),
-				getColorCoding(individual.getGenome().getInactiveAllele(chromosome.ordinal()).isDominant()));
+	protected final void drawRow(String text0, String text1, String text2, IIndividual individual, IChromosomeType chromosome) {
+		drawRow(text0, text1, text2, fontColor.get("gui.screen"), getColorCoding(individual.getGenome().getActiveAllele(chromosome).isDominant()),
+				getColorCoding(individual.getGenome().getInactiveAllele(chromosome).isDominant()));
 	}
 
-	protected final void drawSpeciesRow(String text0, IIndividual individual, Enum<?> chromosome, String customPrimaryName, String customSecondaryName) {
+	protected final void drawSpeciesRow(String text0, IIndividual individual, IChromosomeType chromosome, String customPrimaryName, String customSecondaryName) {
 		IAlleleSpecies primary = individual.getGenome().getPrimary();
 		IAlleleSpecies secondary = individual.getGenome().getSecondary();
 
@@ -116,7 +119,7 @@ public abstract class GuiAlyzer extends GuiForestry<TileForestry> {
 
 	}
 
-	protected final void drawSpeciesRow(String text0, IIndividual individual, Enum<?> chromosome){
+	protected final void drawSpeciesRow(String text0, IIndividual individual, IChromosomeType chromosome){
 		drawSpeciesRow(text0, individual, chromosome, null, null);
 	}
 

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

@@ -12,6 +12,7 @@ package forestry.core.gui;
 
 import java.util.HashMap;
 
+import forestry.api.arboriculture.EnumTreeChromosome;
 import net.minecraft.client.gui.GuiButton;
 import net.minecraft.client.renderer.RenderHelper;
 import net.minecraft.entity.player.EntityPlayer;
@@ -74,9 +75,8 @@ public class GuiNaturalistInventory extends GuiForestry<TileForestry> {
 			startPage();
 
 			displaySpeciesInformation(true, individual.getGenome().getPrimary(), iconStacks.get(individual.getIdent()), 10);
-			if (!individual.isPureBred(0))
-				displaySpeciesInformation(individual.isAnalyzed(), individual.getGenome().getSecondary(), iconStacks.get(individual.getGenome().getSecondary().getUID()),
-						10);
+			if (!individual.isPureBred(EnumTreeChromosome.SPECIES))
+				displaySpeciesInformation(individual.isAnalyzed(), individual.getGenome().getSecondary(), iconStacks.get(individual.getGenome().getSecondary().getUID()), 10);
 
 			endPage();
 		}

src/main/java/forestry/core/inventory/ItemInventory.java

@@ -48,6 +48,25 @@ public class ItemInventory implements IInventory, INBTTagable {
 		readFromNBT(itemstack.getTagCompound());
 	}
 
+	public static int getOccupiedSlotCount(ItemStack itemStack) {
+		NBTTagCompound nbt = itemStack.getTagCompound();
+		if (nbt == null)
+			return 0;
+
+		int count = 0;
+		if (nbt.hasKey("Items")) {
+			NBTTagList nbttaglist = nbt.getTagList("Items", 10);
+			for (int i = 0; i < nbttaglist.tagCount(); i++) {
+				NBTTagCompound nbttagcompound1 = nbttaglist.getCompoundTagAt(i);
+				ItemStack itemStack1 = ItemStack.loadItemStackFromNBT(nbttagcompound1);
+				if (itemStack1 != null && itemStack1.stackSize > 0) {
+					count++;
+				}
+			}
+		}
+		return count;
+	}
+
 	protected void setUID(boolean override) {
 		if (parent.getTagCompound() == null)
 			parent.setTagCompound(new NBTTagCompound());

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

@@ -41,7 +41,7 @@ public class ForestryModEnvWarningCallable implements ICrashCallable {
 			Class<?> c = Class.forName("org.bukkit.Bukkit");
 			modIDs.add("Bukkit, Cauldron, or other Bukkit replacement");
 		}
-		catch (Throwable t) {} // No need to do anything.
+		catch (Throwable ignored) {} // No need to do anything.
 
 		// Add other bad mods here.
 

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

@@ -28,7 +28,6 @@ import net.minecraft.block.Block;
 import net.minecraft.entity.Entity;
 import net.minecraft.entity.EntityList;
 import net.minecraft.entity.EntityLiving;
-import net.minecraft.entity.IEntityLivingData;
 import net.minecraft.entity.item.EntityItem;
 import net.minecraft.entity.player.EntityPlayer;
 import net.minecraft.init.Blocks;
@@ -37,7 +36,6 @@ import net.minecraft.inventory.InventoryLargeChest;
 import net.minecraft.item.ItemStack;
 import net.minecraft.tileentity.TileEntity;
 import net.minecraft.tileentity.TileEntityChest;
-import net.minecraft.util.ChatComponentText;
 import net.minecraft.util.MathHelper;
 import net.minecraft.world.World;
 import net.minecraft.world.biome.BiomeGenBase;
@@ -45,7 +43,6 @@ import net.minecraft.world.biome.BiomeGenBase;
 import java.security.MessageDigest;
 import java.security.cert.Certificate;
 import java.util.Arrays;
-import java.util.Iterator;
 import java.util.Map;
 import java.util.Random;
 
@@ -57,8 +54,7 @@ public class Utils {
 		if (rand == null)
 			rand = new Random();
 
-		int uid = rand.nextInt();
-		return uid;
+		return rand.nextInt();
 	}
 
 	public static void dropInventory(TileForestry tile, World world, int x, int y, int z) {

src/main/java/forestry/factory/gadgets/TileWorktable.java

@@ -43,6 +43,7 @@ public class TileWorktable extends TileBase implements ICrafter {
 
 	/* CONSTANTS */
 	public final static int SLOT_CRAFTING_1 = 0;
+	public final static int SLOT_CRAFTING_COUNT = 9;
 	public final static int SLOT_CRAFTING_RESULT = 9;
 	public final static short SLOT_INVENTORY_1 = 0;
 	public final static short SLOT_INVENTORY_COUNT = 18;
@@ -135,7 +136,7 @@ public class TileWorktable extends TileBase implements ICrafter {
 				return false;
 
 			ItemStack recipeOutput = RECIPE_BRIDGE.findMatchingRecipe(crafting, world);
-			return recipeOutput != null && cachedRecipeOutput.isItemEqual(recipeOutput);
+			return ItemStack.areItemStacksEqual(cachedRecipeOutput, recipeOutput);
 		}
 
 		@Override
@@ -447,7 +448,7 @@ public class TileWorktable extends TileBase implements ICrafter {
 			return false;
 
 		// Need at least one matched set
-		ItemStack[] set = craftingInventory.getStacks(SLOT_CRAFTING_1, 9);
+		ItemStack[] set = craftingInventory.getStacks(SLOT_CRAFTING_1, SLOT_CRAFTING_COUNT);
 		ItemStack[] stock = accessibleInventory.getStacks(SLOT_INVENTORY_1, SLOT_INVENTORY_COUNT);
 		if (StackUtils.containsSets(set, stock, true, true) == 0)
 			return false;
@@ -495,7 +496,7 @@ public class TileWorktable extends TileBase implements ICrafter {
 		if (recipeOutput == null)
 			return false;
 
-		return recipeOutput.isItemEqual(currentRecipe.getRecipeOutput());
+		return ItemStack.areItemStacksEqual(recipeOutput, currentRecipe.getRecipeOutput());
 	}
 
 	private boolean removeResources(EntityPlayer player) {

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

@@ -67,19 +67,19 @@ public class Butterfly extends IndividualLiving implements IButterfly {
 	public void addTooltip(List<String> list) {
 		IAlleleButterflySpecies primary = genome.getPrimary();
 		IAlleleButterflySpecies secondary = genome.getSecondary();
-		if (!isPureBred(EnumButterflyChromosome.SPECIES.ordinal()))
+		if (!isPureBred(EnumButterflyChromosome.SPECIES))
 			list.add("\u00A79" + StringUtil.localize("butterflies.hybrid").replaceAll("%PRIMARY",primary.getName()).replaceAll("%SECONDARY",secondary.getName()));
 
 		if(getMate() != null)
 			list.add("\u00A7c" + StringUtil.localize("gui.fecundated").toUpperCase(Locale.ENGLISH));
-		list.add("\u00A7e" + genome.getActiveAllele(EnumButterflyChromosome.SIZE.ordinal()).getName());
-		list.add("\u00A7f" + genome.getActiveAllele(EnumButterflyChromosome.SPEED.ordinal()).getName() + " " + StringUtil.localize("gui.flyer"));
-		list.add(genome.getActiveAllele(EnumButterflyChromosome.LIFESPAN.ordinal()).getName() + " " + StringUtil.localize("gui.life"));
+		list.add("\u00A7e" + genome.getActiveAllele(EnumButterflyChromosome.SIZE).getName());
+		list.add("\u00A7f" + genome.getActiveAllele(EnumButterflyChromosome.SPEED).getName() + " " + StringUtil.localize("gui.flyer"));
+		list.add(genome.getActiveAllele(EnumButterflyChromosome.LIFESPAN).getName() + " " + StringUtil.localize("gui.life"));
 
-		IAlleleTolerance tempTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE.ordinal());
+		IAlleleTolerance tempTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE);
 		list.add("\u00A7aT: " + AlleleManager.climateHelper.toDisplay(genome.getPrimary().getTemperature()) + " / " + tempTolerance.getName());
 
-		IAlleleTolerance humidTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE.ordinal());
+		IAlleleTolerance humidTolerance = (IAlleleTolerance)getGenome().getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE);
 		list.add("\u00A7aH: " + AlleleManager.climateHelper.toDisplay(genome.getPrimary().getHumidity()) + " / " + humidTolerance.getName());
 
 		list.add("\u00A7c" + GenericRatings.rateActivityTime(genome.getNocturnal(), genome.getPrimary().isNocturnal()));

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

@@ -52,72 +52,72 @@ public class ButterflyGenome extends Genome implements IButterflyGenome {
 	/* SPECIES */
 	@Override
 	public IAlleleButterflySpecies getPrimary() {
-		return (IAlleleButterflySpecies) getActiveAllele(EnumButterflyChromosome.SPECIES.ordinal());
+		return (IAlleleButterflySpecies) getActiveAllele(EnumButterflyChromosome.SPECIES);
 	}
 
 	@Override
 	public IAlleleButterflySpecies getSecondary() {
-		return (IAlleleButterflySpecies) getInactiveAllele(EnumButterflyChromosome.SPECIES.ordinal());
+		return (IAlleleButterflySpecies) getInactiveAllele(EnumButterflyChromosome.SPECIES);
 	}
 
 	@Override
 	public float getSize() {
-		return ((IAlleleFloat) getActiveAllele(EnumButterflyChromosome.SIZE.ordinal())).getValue();
+		return ((IAlleleFloat) getActiveAllele(EnumButterflyChromosome.SIZE)).getValue();
 	}
 	
 	@Override
 	public int getLifespan() {
-		return ((IAlleleInteger) getActiveAllele(EnumButterflyChromosome.LIFESPAN.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumButterflyChromosome.LIFESPAN)).getValue();
 	}
 	
 	@Override
 	public float getSpeed() {
-		return ((IAlleleFloat) getActiveAllele(EnumButterflyChromosome.SPEED.ordinal())).getValue();
+		return ((IAlleleFloat) getActiveAllele(EnumButterflyChromosome.SPEED)).getValue();
 	}
 
 	@Override
 	public int getMetabolism() {
-		return ((IAlleleInteger) getActiveAllele(EnumButterflyChromosome.METABOLISM.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumButterflyChromosome.METABOLISM)).getValue();
 	}
 
 	@Override
 	public int getFertility() {
-		return ((IAlleleInteger) getActiveAllele(EnumButterflyChromosome.FERTILITY.ordinal())).getValue();
+		return ((IAlleleInteger) getActiveAllele(EnumButterflyChromosome.FERTILITY)).getValue();
 	}
 
 	@Override
 	public EnumTolerance getToleranceTemp() {
-		return ((AlleleTolerance) getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE.ordinal())).getValue();
+		return ((AlleleTolerance) getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE)).getValue();
 	}
 
 	@Override
 	public EnumTolerance getToleranceHumid() {
-		return ((AlleleTolerance) getActiveAllele(EnumButterflyChromosome.HUMIDITY_TOLERANCE.ordinal())).getValue();
+		return ((AlleleTolerance) getActiveAllele(EnumButterflyChromosome.HUMIDITY_TOLERANCE)).getValue();
 	}
 
 	@Override
 	public boolean getNocturnal() {
-		return ((AlleleBoolean) getActiveAllele(EnumButterflyChromosome.NOCTURNAL.ordinal())).getValue();
+		return ((AlleleBoolean) getActiveAllele(EnumButterflyChromosome.NOCTURNAL)).getValue();
 	}
 
 	@Override
 	public boolean getTolerantFlyer() {
-		return ((AlleleBoolean) getActiveAllele(EnumButterflyChromosome.TOLERANT_FLYER.ordinal())).getValue();
+		return ((AlleleBoolean) getActiveAllele(EnumButterflyChromosome.TOLERANT_FLYER)).getValue();
 	}
 
 	@Override
 	public boolean getFireResist() {
-		return ((AlleleBoolean) getActiveAllele(EnumButterflyChromosome.FIRE_RESIST.ordinal())).getValue();
+		return ((AlleleBoolean) getActiveAllele(EnumButterflyChromosome.FIRE_RESIST)).getValue();
 	}
 
 	@Override
 	public IFlowerProvider getFlowerProvider() {
-		return ((IAlleleFlowers) getActiveAllele(EnumButterflyChromosome.FLOWER_PROVIDER.ordinal())).getProvider();
+		return ((IAlleleFlowers) getActiveAllele(EnumButterflyChromosome.FLOWER_PROVIDER)).getProvider();
 	}
 
 	@Override
 	public IAlleleButterflyEffect getEffect() {
-		return (IAlleleButterflyEffect) getActiveAllele(EnumButterflyChromosome.EFFECT.ordinal());
+		return (IAlleleButterflyEffect) getActiveAllele(EnumButterflyChromosome.EFFECT);
 	}
 
 	@Override

src/main/java/forestry/lepidopterology/gui/GuiFlutterlyzer.java

@@ -12,7 +12,6 @@ package forestry.lepidopterology.gui;
 
 import forestry.api.genetics.AlleleManager;
 import forestry.api.genetics.IAllele;
-import forestry.api.genetics.IAlleleEffect;
 import forestry.api.genetics.IAlleleFlowers;
 import forestry.api.genetics.IAlleleInteger;
 import forestry.api.genetics.IAlleleTolerance;
@@ -39,10 +38,7 @@ import java.util.Map;
 public class GuiFlutterlyzer extends GuiAlyzer {
 
 	public GuiFlutterlyzer(EntityPlayer player, FlutterlyzerInventory inventory) {
-		super(AlleleManager.alleleRegistry.getSpeciesRoot("rootButterflies"), player,
-				new ContainerFlutterlyzer(player.inventory, inventory), inventory, 1, inventory.getSizeInventory());
-
-		guiName = "gui.flutterlyzer";
+		super("rootButterflies", player, new ContainerFlutterlyzer(player.inventory, inventory), inventory, "gui.flutterlyzer");
 
 		ArrayList<ItemStack> butterflyList = new ArrayList<ItemStack>();
 		((ItemButterflyGE) ForestryItem.butterflyGE.item()).addCreativeItems(butterflyList, false);
@@ -105,33 +101,33 @@ public class GuiFlutterlyzer extends GuiAlyzer {
 		drawSpeciesRow(StringUtil.localize("gui.species"), butterfly, EnumButterflyChromosome.SPECIES);
 		newLine();
 
-		drawRow(StringUtil.localize("gui.size"), butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.SIZE.ordinal()).getName(),
-				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.SIZE.ordinal()).getName(), butterfly, EnumButterflyChromosome.SPEED);
+		drawRow(StringUtil.localize("gui.size"), butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.SIZE).getName(),
+				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.SIZE).getName(), butterfly, EnumButterflyChromosome.SPEED);
 
-		drawRow(StringUtil.localize("gui.lifespan"), butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.LIFESPAN.ordinal()).getName(),
-				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.LIFESPAN.ordinal()).getName(), butterfly,
+		drawRow(StringUtil.localize("gui.lifespan"), butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.LIFESPAN).getName(),
+				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.LIFESPAN).getName(), butterfly,
 				EnumButterflyChromosome.LIFESPAN);
 
-		drawRow(StringUtil.localize("gui.speed"), butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.SPEED.ordinal()).getName(),
-				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.SPEED.ordinal()).getName(), butterfly, EnumButterflyChromosome.SPEED);
+		drawRow(StringUtil.localize("gui.speed"), butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.SPEED).getName(),
+				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.SPEED).getName(), butterfly, EnumButterflyChromosome.SPEED);
 
 		drawRow(StringUtil.localize("gui.metabolism"), GenericRatings.rateMetabolism(butterfly.getGenome().getMetabolism()),
-				GenericRatings.rateMetabolism(((IAlleleInteger) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.METABOLISM.ordinal())).getValue()), butterfly, EnumButterflyChromosome.METABOLISM);
+				GenericRatings.rateMetabolism(((IAlleleInteger) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.METABOLISM)).getValue()), butterfly, EnumButterflyChromosome.METABOLISM);
 
 		drawLine(StringUtil.localize("gui.fertility"), COLUMN_0);
-		drawFertilityInfo(butterfly.getGenome().getFertility(), COLUMN_1, getColorCoding(butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.FERTILITY.ordinal())
+		drawFertilityInfo(butterfly.getGenome().getFertility(), COLUMN_1, getColorCoding(butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.FERTILITY)
 				.isDominant()), 8);
-		drawFertilityInfo(((IAlleleInteger) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.FERTILITY.ordinal())).getValue(), COLUMN_2, getColorCoding(butterfly
-				.getGenome().getInactiveAllele(EnumButterflyChromosome.FERTILITY.ordinal()).isDominant()), 8);
+		drawFertilityInfo(((IAlleleInteger) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.FERTILITY)).getValue(), COLUMN_2, getColorCoding(butterfly
+				.getGenome().getInactiveAllele(EnumButterflyChromosome.FERTILITY).isDominant()), 8);
 
 		newLine();
 
 		drawRow(StringUtil.localize("gui.flowers"), butterfly.getGenome().getFlowerProvider().getDescription(),
-				((IAlleleFlowers) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.FLOWER_PROVIDER.ordinal())).getProvider()
+				((IAlleleFlowers) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.FLOWER_PROVIDER)).getProvider()
 						.getDescription(), butterfly, EnumButterflyChromosome.FLOWER_PROVIDER);
 
 		drawRow(StringUtil.localize("gui.effect"), butterfly.getGenome().getEffect().getName(),
-				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.EFFECT.ordinal()).getName(), butterfly,
+				butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.EFFECT).getName(), butterfly,
 				EnumButterflyChromosome.EFFECT);
 
 		newLine();
@@ -152,8 +148,8 @@ public class GuiFlutterlyzer extends GuiAlyzer {
 		drawRow(StringUtil.localize("gui.climate"), AlleleManager.climateHelper.toDisplay(butterfly.getGenome().getPrimary().getTemperature()),
 				AlleleManager.climateHelper.toDisplay(butterfly.getGenome().getPrimary().getTemperature()), butterfly, EnumButterflyChromosome.SPECIES);
 
-		IAlleleTolerance tempToleranceActive = (IAlleleTolerance)butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE.ordinal());
-		IAlleleTolerance tempToleranceInactive = (IAlleleTolerance)butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE.ordinal());
+		IAlleleTolerance tempToleranceActive = (IAlleleTolerance)butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE);
+		IAlleleTolerance tempToleranceInactive = (IAlleleTolerance)butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.TEMPERATURE_TOLERANCE);
 		drawLine(StringUtil.localize("gui.temptol"), COLUMN_0);
 		drawToleranceInfo(tempToleranceActive, COLUMN_1);
 		drawToleranceInfo(tempToleranceInactive, COLUMN_2);
@@ -163,8 +159,8 @@ public class GuiFlutterlyzer extends GuiAlyzer {
 		drawRow(StringUtil.localize("gui.humidity"), AlleleManager.climateHelper.toDisplay(butterfly.getGenome().getPrimary().getHumidity()),
 				AlleleManager.climateHelper.toDisplay(butterfly.getGenome().getPrimary().getHumidity()), butterfly, EnumButterflyChromosome.SPECIES);
 
-		IAlleleTolerance humidToleranceActive = (IAlleleTolerance)butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.HUMIDITY_TOLERANCE.ordinal());
-		IAlleleTolerance humidToleranceInactive = (IAlleleTolerance)butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.HUMIDITY_TOLERANCE.ordinal());
+		IAlleleTolerance humidToleranceActive = (IAlleleTolerance)butterfly.getGenome().getActiveAllele(EnumButterflyChromosome.HUMIDITY_TOLERANCE);
+		IAlleleTolerance humidToleranceInactive = (IAlleleTolerance)butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.HUMIDITY_TOLERANCE);
 		drawLine(StringUtil.localize("gui.humidtol"), COLUMN_0);
 		drawToleranceInfo(humidToleranceActive, COLUMN_1);
 		drawToleranceInfo(humidToleranceInactive, COLUMN_2);
@@ -182,7 +178,7 @@ public class GuiFlutterlyzer extends GuiAlyzer {
 			nocturnal0 = butterfly.getGenome().getPrimary().isNocturnal() ? yes : no;
 			diurnal0 = !butterfly.getGenome().getPrimary().isNocturnal() ? yes : no;
 		}
-		if(((AlleleBoolean) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.NOCTURNAL.ordinal())).getValue()) {
+		if(((AlleleBoolean) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.NOCTURNAL)).getValue()) {
 			nocturnal1 = diurnal1 = yes;
 		} else {
 			nocturnal1 = butterfly.getGenome().getSecondary().isNocturnal() ? yes : no;
@@ -200,13 +196,13 @@ public class GuiFlutterlyzer extends GuiAlyzer {
 		newLine();
 
 		String primary = StringUtil.readableBoolean(butterfly.getGenome().getTolerantFlyer(), yes, no);
-		String secondary = StringUtil.readableBoolean(((AlleleBoolean) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.TOLERANT_FLYER.ordinal())).getValue(), yes,
+		String secondary = StringUtil.readableBoolean(((AlleleBoolean) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.TOLERANT_FLYER)).getValue(), yes,
 				no);
 
 		drawRow(StringUtil.localize("gui.flyer"), primary, secondary, butterfly, EnumButterflyChromosome.TOLERANT_FLYER);
 
 		primary = StringUtil.readableBoolean(butterfly.getGenome().getFireResist(), yes, no);
-		secondary = StringUtil.readableBoolean(((AlleleBoolean) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.FIRE_RESIST.ordinal())).getValue(), yes,
+		secondary = StringUtil.readableBoolean(((AlleleBoolean) butterfly.getGenome().getInactiveAllele(EnumButterflyChromosome.FIRE_RESIST)).getValue(), yes,
 				no);
 
 		drawRow(StringUtil.localize("gui.fireresist"), primary, secondary, butterfly, EnumButterflyChromosome.FIRE_RESIST);

src/main/java/forestry/pipes/PipeItemsPropolis.java

@@ -147,7 +147,7 @@ public class PipeItemsPropolis extends Pipe<PipeTransportItems> {
 		// A bit of speed to perhaps prevent bees from popping out of the pipe.
 		try {
 			event.item.setSpeed(TransportConstants.PIPE_NORMAL_SPEED * 20F);
-		} catch (Throwable error) {
+		} catch (Throwable ignored) {
 		}
 	}
 

src/main/java/forestry/pipes/PipeLogicPropolis.java

@@ -86,19 +86,19 @@ public class PipeLogicPropolis {
 		// Special bee filtering
 		if (bee != null) {
 			if (filter == EnumFilterType.PURE_BREED)
-				return bee.isPureBred(EnumBeeChromosome.SPECIES.ordinal());
+				return bee.isPureBred(EnumBeeChromosome.SPECIES);
 			if (filter == EnumFilterType.NOCTURNAL)
 				return bee.getGenome().getNocturnal();
 			if (filter == EnumFilterType.PURE_NOCTURNAL)
-				return bee.getGenome().getNocturnal() && bee.isPureBred(EnumBeeChromosome.NOCTURNAL.ordinal());
+				return bee.getGenome().getNocturnal() && bee.isPureBred(EnumBeeChromosome.NOCTURNAL);
 			if (filter == EnumFilterType.FLYER)
 				return bee.getGenome().getTolerantFlyer();
 			if (filter == EnumFilterType.PURE_FLYER)
-				return bee.getGenome().getTolerantFlyer() && bee.isPureBred(EnumBeeChromosome.TOLERANT_FLYER.ordinal());
+				return bee.getGenome().getTolerantFlyer() && bee.isPureBred(EnumBeeChromosome.TOLERANT_FLYER);
 			if (filter == EnumFilterType.CAVE)
 				return bee.getGenome().getCaveDwelling();
 			if (filter == EnumFilterType.PURE_CAVE)
-				return bee.getGenome().getCaveDwelling() && bee.isPureBred(EnumBeeChromosome.CAVE_DWELLING.ordinal());
+				return bee.getGenome().getCaveDwelling() && bee.isPureBred(EnumBeeChromosome.CAVE_DWELLING);
 			if (filter == EnumFilterType.NATURAL)
 				return bee.isNatural();
 		}

src/main/java/forestry/plugins/PluginApiculture.java

@@ -82,6 +82,7 @@ import forestry.apiculture.genetics.AlleleEffectRadioactive;
 import forestry.apiculture.genetics.AlleleEffectRepulsion;
 import forestry.apiculture.genetics.AlleleEffectResurrection;
 import forestry.apiculture.genetics.AlleleEffectSnowing;
+import forestry.apiculture.genetics.AlleleEffectFertile;
 import forestry.apiculture.genetics.AlleleFlowers;
 import forestry.apiculture.genetics.Bee;
 import forestry.apiculture.genetics.BeeHelper;
@@ -1028,8 +1029,10 @@ public class PluginApiculture extends ForestryPlugin {
 		// Agrarian branch
 		Allele.speciesRural = new AlleleBeeSpecies("speciesRural", false, "bees.species.rural", agrarian, "rustico", 0xfeff8f, 0xffdc16).addProduct(
 				ForestryItem.beeComb.getItemStack(1, 14), 20).setIsSecret();
-		// 41 Farmerly
-		// 42 Agrarian
+		Allele.speciesFarmerly = new AlleleBeeSpecies("speciesFarmerly", true, "bees.species.farmerly", agrarian, "arator", 0xD39728, 0xffdc16).addProduct(
+				ForestryItem.beeComb.getItemStack(1, 14), 27).setIsSecret();
+		Allele.speciesArgrarian = new AlleleBeeSpecies("speciesArgrarian", true, "bees.species.agrarian", agrarian, "arator", 0xFFCA75, 0xFFE047).addProduct(
+				ForestryItem.beeComb.getItemStack(1, 14), 35).setIsSecret().setHasEffect();
 
 		// Boggy branch
 		Allele.speciesMarshy = new AlleleBeeSpecies("speciesMarshy", true, "bees.species.marshy", boggy, "adorasti", 0x546626, 0xffdc16).addProduct(
@@ -1075,6 +1078,7 @@ public class PluginApiculture extends ForestryPlugin {
 		Allele.effectReanimation = new AlleleEffectResurrection("effectReanimation", "reanimation", AlleleEffectResurrection.getReanimationList());
 		Allele.effectResurrection = new AlleleEffectResurrection("effectResurrection", "resurrection", AlleleEffectResurrection.getResurrectionList());
 		Allele.effectRepulsion = new AlleleEffectRepulsion("effectRepulsion");
+		Allele.effectFertile = new AlleleEffectFertile("effectFertile");
 
 	}
 
@@ -1160,6 +1164,10 @@ public class PluginApiculture extends ForestryPlugin {
 		// Agrarian branch
 		BeeTemplates.ruralA = new BeeMutation(Allele.speciesMeadows, Allele.speciesDiligent, BeeTemplates.getRuralTemplate(), 12)
 				.restrictBiomeType(BiomeDictionary.Type.PLAINS).enableStrictBiomeCheck();
+		new BeeMutation(Allele.speciesRural, Allele.speciesUnweary, BeeTemplates.getFarmerlyTemplate(), 10)
+				.restrictBiomeType(BiomeDictionary.Type.PLAINS).enableStrictBiomeCheck();
+		new BeeMutation(Allele.speciesFarmerly, Allele.speciesIndustrious, BeeTemplates.getAgrarianTemplate(), 6)
+				.restrictBiomeType(BiomeDictionary.Type.PLAINS).enableStrictBiomeCheck();
 
 		// Monastic branch
 		BeeTemplates.secludedA = new BeeMutation(Allele.speciesMonastic, Allele.speciesAustere, BeeTemplates.getSecludedTemplate(), 12);
@@ -1210,6 +1218,8 @@ public class PluginApiculture extends ForestryPlugin {
 		beeInterface.registerTemplate(BeeTemplates.getReddenedTemplate());
 		beeInterface.registerTemplate(BeeTemplates.getOmegaTemplate());
 		beeInterface.registerTemplate(BeeTemplates.getRuralTemplate());
+		beeInterface.registerTemplate(BeeTemplates.getFarmerlyTemplate());
+		beeInterface.registerTemplate(BeeTemplates.getAgrarianTemplate());
 		beeInterface.registerTemplate(BeeTemplates.getLeporineTemplate());
 		beeInterface.registerTemplate(BeeTemplates.getMerryTemplate());
 		beeInterface.registerTemplate(BeeTemplates.getTipsyTemplate());

src/main/java/forestry/plugins/PluginIC2.java

@@ -173,12 +173,6 @@ public class PluginIC2 extends ForestryPlugin {
 		ChipsetManager.circuitRegistry.registerLegacyMapping(CircuitId.ELECTRIC_EFFICIENCY_I, "forestry.energyEfficiency1");
 		ChipsetManager.circuitRegistry.registerLegacyMapping(CircuitId.ELECTRIC_BOOST_I, "forestry.energyBoost1");
 		ChipsetManager.circuitRegistry.registerLegacyMapping(CircuitId.ELECTRIC_BOOST_II, "forestry.energyBoost2");
-
-		// Remove some items from the recycler
-		if (PluginManager.Module.APICULTURE.isEnabled()) {
-			Recipes.recyclerBlacklist.add(new RecipeInputItemStack(ForestryItem.beeQueenGE.getItemStack()));
-			Recipes.recyclerBlacklist.add(new RecipeInputItemStack(ForestryItem.beePrincessGE.getItemStack()));
-		}
 	}
 
 	@Override
@@ -188,6 +182,16 @@ public class PluginIC2 extends ForestryPlugin {
 
 		config = Config.config;
 
+		// Remove some items from the recycler
+		if (Recipes.recyclerBlacklist != null) {
+			if (PluginManager.Module.APICULTURE.isEnabled()) {
+				Recipes.recyclerBlacklist.add(new RecipeInputItemStack(ForestryItem.beeQueenGE.getItemStack()));
+				Recipes.recyclerBlacklist.add(new RecipeInputItemStack(ForestryItem.beePrincessGE.getItemStack()));
+			}
+		} else {
+			Proxies.log.severe("IC2 Recipes.recyclerBlacklist not found.");
+		}
+
 		definitionEngineTin.register();
 		definitionGenerator.register();
 

src/main/java/forestry/storage/items/ItemBackpack.java

@@ -85,10 +85,7 @@ public class ItemBackpack extends ItemInventoried {
 
 	@Override
 	public boolean onItemUse(ItemStack itemstack, EntityPlayer player, World world, int x, int y, int z, int side, float hitX, float hitY, float hitZ) {
-		if (getInventoryHit(world, x, y, z, side) != null)
-			return true;
-		else
-			return false;
+		return getInventoryHit(world, x, y, z, side) != null;
 	}
 
 	@Override
@@ -222,21 +219,7 @@ public class ItemBackpack extends ItemInventoried {
 	@SuppressWarnings({"rawtypes", "unchecked"})
 	@Override
 	public void addInformation(ItemStack itemstack, EntityPlayer player, List list, boolean flag) {
-		ItemInventory inventory = new ItemInventory(ItemBackpack.class, getBackpackSize(), itemstack);
-
-		// HashMap<ItemStack, Integer> contents = new HashMap<ItemStack,
-		// Integer>();
-		int occupied = 0;
-
-		for (int i = 0; i < inventory.getSizeInventory(); i++) {
-			if (inventory.getStackInSlot(i) == null)
-				continue;
-			if (inventory.getStackInSlot(i).stackSize <= 0)
-				continue;
-
-			// Count the slot as occupied
-			occupied++;
-		}
+		int occupied = ItemInventory.getOccupiedSlotCount(itemstack);
 
 		BackpackMode mode = getMode(itemstack);
 		if (mode == BackpackMode.LOCKED)