Fix #431 Leaves become invisible when they start to decay

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

@@ -50,7 +50,7 @@ public class ItemBeeGE extends ItemGE {
 	}
 
 	@Override
-	protected IIndividual getIndividual(ItemStack itemstack) {
+	public IBee getIndividual(ItemStack itemstack) {
 		return new Bee(itemstack.getTagCompound());
 	}
 

src/main/java/forestry/arboriculture/PacketHandlerArboriculture.java

@@ -12,9 +12,12 @@ package forestry.arboriculture;
 
 import forestry.arboriculture.gadgets.TileLeaves;
 import forestry.arboriculture.network.PacketLeafUpdate;
+import forestry.arboriculture.network.PacketRipeningUpdate;
 import forestry.core.interfaces.IPacketHandler;
 import forestry.core.network.PacketIds;
 import forestry.core.proxy.Proxies;
+import forestry.storage.proxy.ProxyStorage;
+
 import java.io.DataInputStream;
 import net.minecraft.entity.player.EntityPlayer;
 import net.minecraft.tileentity.TileEntity;
@@ -26,11 +29,18 @@ public class PacketHandlerArboriculture implements IPacketHandler {
 		try {
 
 			switch (packetID) {
-			case PacketIds.LEAF_UPDATE:
-				PacketLeafUpdate packet = new PacketLeafUpdate();
-				packet.readData(data);
-				onLeafUpdate(packet);
-				break;
+				case PacketIds.LEAF_UPDATE: {
+					PacketLeafUpdate packet = new PacketLeafUpdate();
+					packet.readData(data);
+					onLeafUpdate(packet);
+					break;
+				}
+				case PacketIds.RIPENING_UPDATE: {
+					PacketRipeningUpdate packet = new PacketRipeningUpdate();
+					packet.readData(data);
+					onRipeningUpdate(packet);
+					break;
+				}
 			}
 
 		} catch(Exception ex) {
@@ -46,5 +56,12 @@ public class PacketHandlerArboriculture implements IPacketHandler {
 
 	}
 
+	private void onRipeningUpdate(PacketRipeningUpdate packet) {
+
+		TileEntity tile = packet.getTarget(Proxies.common.getRenderWorld());
+		if (tile instanceof TileLeaves)
+			((TileLeaves) tile).fromRipeningPacket(packet);
+
+	}
 
 }

src/main/java/forestry/arboriculture/gadgets/ForestryBlockLeaves.java

@@ -181,6 +181,7 @@ public class ForestryBlockLeaves extends BlockNewLeaf implements ITileEntityProv
 		if (getLeafTile(world, x, y, z).isDecorative())
 			return;
 		super.beginLeavesDecay(world, x, y, z);
+		world.markBlockForUpdate(x, y, z);
 	}
 
 	@Override
@@ -191,6 +192,11 @@ public class ForestryBlockLeaves extends BlockNewLeaf implements ITileEntityProv
 
 		super.updateTick(world, x, y, z, random);
 
+		// check leaves tile again because they can decay in super.updateTick
+		tileLeaves = getLeafTile(world, x, y, z);
+		if (tileLeaves == null)
+			return;
+
 		if (world.rand.nextFloat() > 0.1)
 			return;
 		tileLeaves.onBlockTick();

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

@@ -48,6 +48,7 @@ import forestry.api.lepidopterology.IButterfly;
 import forestry.api.lepidopterology.IButterflyNursery;
 import forestry.api.lepidopterology.IButterflyRoot;
 import forestry.arboriculture.network.PacketLeafUpdate;
+import forestry.arboriculture.network.PacketRipeningUpdate;
 import forestry.core.utils.GeneticsUtil;
 import forestry.core.EnumErrorCode;
 import forestry.core.genetics.Allele;
@@ -312,27 +313,26 @@ public class TileLeaves extends TileTreeContainer implements IPollinatable, IFru
 	}
 
 	private void sendNetworkUpdateRipening() {
-		Proxies.net.sendNetworkPacket(new PacketLeafUpdate(this, determineFruitColour()), xCoord, yCoord, zCoord);
+		Proxies.net.sendNetworkPacket(new PacketRipeningUpdate(this, determineFruitColour()), xCoord, yCoord, zCoord);
 	}
 
 	@Override
 	public void fromPacket(ForestryPacket packetRaw) {
+		super.fromPacket(packetRaw);
 
 		PacketLeafUpdate packet = (PacketLeafUpdate)packetRaw;
-		if(packet.isRipeningUpdate()) {
-			colourFruits = packet.colourFruits;
-		} else {
-			readFromNBT(packet.getTagCompound());
-			isFruitLeaf = packet.isFruitLeaf();
-			isPollinatedState = packet.isPollinated();
-			textureIndexFancy = packet.textureIndexFancy;
-			textureIndexPlain = packet.textureIndexPlain;
-			textureIndexFruits = packet.textureIndexFruit;
-			colourLeaves = packet.colourLeaves;
-			colourFruits = packet.colourFruits;
-		}
 
-		worldObj.func_147479_m(xCoord, yCoord, zCoord);
+		isFruitLeaf = packet.isFruitLeaf();
+		isPollinatedState = packet.isPollinated();
+		textureIndexFancy = packet.textureIndexFancy;
+		textureIndexPlain = packet.textureIndexPlain;
+		textureIndexFruits = packet.textureIndexFruit;
+		colourLeaves = packet.colourLeaves;
+		colourFruits = packet.colourFruits;
+	}
+
+	public void fromRipeningPacket(PacketRipeningUpdate packet) {
+		colourFruits = packet.colourFruits;
 	}
 
 	/**

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

@@ -45,6 +45,7 @@ import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IIndividual;
 import forestry.api.genetics.IMutation;
 import forestry.arboriculture.gadgets.BlockFruitPod;
+import forestry.arboriculture.gadgets.ForestryBlockLeaves;
 import forestry.arboriculture.gadgets.TileFruitPod;
 import forestry.arboriculture.gadgets.TileLeaves;
 import forestry.arboriculture.gadgets.TileSapling;
@@ -214,20 +215,19 @@ public class TreeHelper extends SpeciesRoot implements ITreeRoot {
 		if (!ForestryBlock.leaves.isBlockEqual(world, x, y, z))
 			return false;
 
-		TileLeaves tileLeaves = new TileLeaves();
-		tileLeaves.setTree((ITree) tree.copy());
-		tileLeaves.setOwner(owner);
-		if (decorative)
-			tileLeaves.setDecorative();
-
-		world.setTileEntity(x, y, z, tileLeaves);
-
-		TileEntity tile = world.getTileEntity(x, y, z);
-		if (!(tile instanceof TileLeaves)) {
+		TileEntity tile = ForestryBlockLeaves.getLeafTile(world, x, y, z);
+		if (tile == null) {
 			world.setBlockToAir(x, y, z);
 			return false;
 		}
 
+		TileLeaves tileLeaves = (TileLeaves) tile;
+		tileLeaves.setOwner(owner);
+		tileLeaves.setTree((ITree) tree.copy());
+		if (decorative)
+			tileLeaves.setDecorative();
+		world.markBlockForUpdate(x, y, z);
+
 		return true;
 	}
 

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

@@ -51,7 +51,7 @@ public class ItemGermlingGE extends ItemGE implements IVariableFermentable {
 	}
 
 	@Override
-	protected IIndividual getIndividual(ItemStack itemstack) {
+	public ITree getIndividual(ItemStack itemstack) {
 		return new Tree(itemstack.getTagCompound());
 	}
 

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

@@ -18,7 +18,6 @@ import net.minecraft.world.World;
 import forestry.api.arboriculture.ITree;
 import forestry.api.core.ForestryAPI;
 import forestry.api.core.Tabs;
-import forestry.api.genetics.AlleleManager;
 import forestry.core.EnumErrorCode;
 import forestry.core.config.Config;
 import forestry.core.interfaces.IErrorSource;
@@ -28,7 +27,6 @@ import forestry.core.items.ItemInventoried;
 import forestry.core.network.GuiId;
 import forestry.core.proxy.Proxies;
 import forestry.core.utils.GeneticsUtil;
-import forestry.core.utils.StackUtils;
 import forestry.plugins.PluginArboriculture;
 
 public class ItemTreealyzer extends ItemInventoried {
@@ -42,7 +40,7 @@ public class ItemTreealyzer extends ItemInventoried {
 
 		@Override
 		protected boolean isSpecimen(ItemStack itemStack) {
-			return StackUtils.containsItemStack(AlleleManager.ersatzSaplings.keySet(), itemStack) || PluginArboriculture.treeInterface.isMember(itemStack);
+			return GeneticsUtil.getGeneticEquivalent(itemStack) instanceof ITree;
 		}
 
 		private void tryAnalyze() {

src/main/java/forestry/arboriculture/network/PacketLeafUpdate.java

@@ -10,17 +10,21 @@
  ******************************************************************************/
 package forestry.arboriculture.network;
 
-import forestry.arboriculture.gadgets.TileLeaves;
-import forestry.core.network.PacketIds;
-import forestry.core.network.PacketTileNBT;
 import java.io.DataInputStream;
 import java.io.DataOutputStream;
 import java.io.IOException;
 
+import net.minecraft.world.World;
+
+import forestry.arboriculture.gadgets.TileLeaves;
+import forestry.core.network.PacketIds;
+import forestry.core.network.PacketTileNBT;
+
 public class PacketLeafUpdate extends PacketTileNBT {
 
-	public byte isRipeningUpdate = 0;
-	
+	private static short hasFruitFlag = 1;
+	private static short isPollinatedFlag = 1 << 1;
+
 	private byte leafState = 0;
 	public short textureIndexFancy;
 	public short textureIndexPlain;
@@ -37,9 +41,9 @@ public class PacketLeafUpdate extends PacketTileNBT {
 
 		leafState = 0;
 		if(leaves.hasFruit())
-			leafState |= 1 << 0;
+			leafState |= hasFruitFlag;
 		if(leaves.isPollinated())
-			leafState |= 1 << 1;
+			leafState |= isPollinatedFlag;
 		textureIndexFancy = leaves.determineTextureIndex(true);
 		textureIndexPlain = leaves.determineTextureIndex(false);
 		textureIndexFruit = leaves.determineOverlayIndex();
@@ -47,56 +51,35 @@ public class PacketLeafUpdate extends PacketTileNBT {
 		colourFruits = leaves.determineFruitColour();
 	}
 
-	public PacketLeafUpdate(TileLeaves leaves, int fruitColour) {
-		super(PacketIds.LEAF_UPDATE, leaves);
-
-		isRipeningUpdate = 1;
-		colourFruits = fruitColour;
-	}
-
 	@Override
 	public void writeData(DataOutputStream data) throws IOException {
 		super.writeData(data);
 
-		data.writeByte(isRipeningUpdate);
-
-		if(isRipeningUpdate()) {
-			data.writeInt(colourFruits);
-		} else {
-			data.writeByte(leafState);
-			data.writeShort(textureIndexFancy);
-			data.writeShort(textureIndexPlain);
-			data.writeShort(textureIndexFruit);
-			data.writeInt(colourLeaves);
-			data.writeInt(colourFruits);
-		}
+		data.writeByte(leafState);
+		data.writeShort(textureIndexFancy);
+		data.writeShort(textureIndexPlain);
+		data.writeShort(textureIndexFruit);
+		data.writeInt(colourLeaves);
+		data.writeInt(colourFruits);
 	}
 	
 	@Override
 	public void readData(DataInputStream data) throws IOException {
 		super.readData(data);
-		
-		isRipeningUpdate = data.readByte();
-		if(isRipeningUpdate()) {
-			colourFruits = data.readInt();
-		} else {
-			leafState = data.readByte();
-			textureIndexFancy = data.readShort();
-			textureIndexPlain = data.readShort();
-			textureIndexFruit = data.readShort();
-			colourLeaves = data.readInt();
-			colourFruits = data.readInt();
-		}
+
+		leafState = data.readByte();
+		textureIndexFancy = data.readShort();
+		textureIndexPlain = data.readShort();
+		textureIndexFruit = data.readShort();
+		colourLeaves = data.readInt();
+		colourFruits = data.readInt();
 	}
-	
-	public boolean isRipeningUpdate() {
-		return isRipeningUpdate != 0;
-	}
-	
+
 	public boolean isFruitLeaf() {
-		return (leafState & (1 << 0)) > 0;
+		return (leafState & hasFruitFlag) > 0;
 	}
+
 	public boolean isPollinated() {
-		return (leafState & (1 << 1)) > 0;
+		return (leafState & isPollinatedFlag) > 0;
 	}
 }

src/main/java/forestry/arboriculture/network/PacketRipeningUpdate.java

@@ -0,0 +1,63 @@
+/*******************************************************************************
+ * 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.network;
+
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.IOException;
+
+import net.minecraft.tileentity.TileEntity;
+import net.minecraft.world.World;
+
+import forestry.arboriculture.gadgets.TileLeaves;
+import forestry.core.network.ForestryPacket;
+import forestry.core.network.PacketIds;
+
+public class PacketRipeningUpdate extends ForestryPacket {
+
+	public int colourFruits;
+	private int posX, posY, posZ;
+
+	public PacketRipeningUpdate() {
+	}
+
+	public PacketRipeningUpdate(TileLeaves leaves, int fruitColour) {
+		super(PacketIds.RIPENING_UPDATE);
+		posX = leaves.xCoord;
+		posY = leaves.yCoord;
+		posZ = leaves.zCoord;
+		colourFruits = fruitColour;
+	}
+
+	@Override
+	public void writeData(DataOutputStream data) throws IOException {
+		super.writeData(data);
+
+		data.writeInt(posX);
+		data.writeInt(posY);
+		data.writeInt(posZ);
+		data.writeInt(colourFruits);
+	}
+
+	@Override
+	public void readData(DataInputStream data) throws IOException {
+		super.readData(data);
+
+		posX = data.readInt();
+		posY = data.readInt();
+		posZ = data.readInt();
+		colourFruits = data.readInt();
+	}
+
+	public TileEntity getTarget(World world) {
+		return world.getTileEntity(posX, posY, posZ);
+	}
+}

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

@@ -24,8 +24,6 @@ public class BlockTypeVoid extends BlockType {
 	@Override
 	public void setBlock(World world, ITreeGenData tree, int x, int y, int z) {
 		world.setBlockToAir(x, y, z);
-		if (world.getTileEntity(x, y, z) != null)
-			world.removeTileEntity(x, y, z);
 	}
 
 }

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

@@ -88,20 +88,14 @@ public abstract class WorldGenArboriculture extends WorldGenBase {
 
 	protected void generateTreeTrunk(int height, int girth, float vines) {
 		int offset = (girth - 1) / 2;
-		for (int x = 0; x < girth; x++)
-			for (int y = 0; y < girth; y++)
-				for (int i = 0; i < height; i++) {
-					addWood(x - offset, i, y - offset, EnumReplaceMode.ALL);
-
-					if (rand.nextFloat() < vines)
-						addVine(x - offset - 1, i, y - offset);
-					if (rand.nextFloat() < vines)
-						addVine(x - offset + 1, i, y - offset);
-					if (rand.nextFloat() < vines)
-						addVine(x - offset, i, y - offset - 1);
-					if (rand.nextFloat() < vines)
-						addVine(x - offset, i, y - offset + 1);
+		for (int x = 0; x < girth; x++) {
+			for (int z = 0; z < girth; z++) {
+				for (int y = 0; y < height; y++) {
+					addWood(x - offset, y, z - offset, EnumReplaceMode.ALL);
+					addVines(x - offset, y, z - offset, vines);
 				}
+			}
+		}
 
 		if (!spawnPods)
 			return;
@@ -148,7 +142,7 @@ public abstract class WorldGenArboriculture extends WorldGenBase {
 	@Override
 	protected void addBlock(int x, int y, int z, BlockType type, EnumReplaceMode replace) {
 		if (replace == EnumReplaceMode.ALL
-				|| replace == EnumReplaceMode.SOFT && Utils.isReplaceableBlock(world, startX + x, startY + y, startZ + z)
+				|| (replace == EnumReplaceMode.SOFT && Utils.isReplaceableBlock(world, startX + x, startY + y, startZ + z))
 				|| world.isAirBlock(startX + x, startY + y, startZ + z))
 			type.setBlock(world, tree, startX + x, startY + y, startZ + z);
 	}
@@ -179,4 +173,18 @@ public abstract class WorldGenArboriculture extends WorldGenBase {
 		addBlock(x, y, z, vine, EnumReplaceMode.NONE);
 	}
 
+	protected final void addVines(int x, int y, int z, float chance) {
+		if (chance <= 0)
+			return;
+
+		if (rand.nextFloat() < chance)
+			addVine(x - 1, y, z);
+		if (rand.nextFloat() < chance)
+			addVine(x + 1, y, z);
+		if (rand.nextFloat() < chance)
+			addVine(x, y, z - 1);
+		if (rand.nextFloat() < chance)
+			addVine(x, y, z + 1);
+	}
+
 }

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

@@ -35,7 +35,7 @@ public abstract class ItemGE extends Item {
 
 	protected abstract int getDefaultSecondaryColour();
 
-	protected abstract IIndividual getIndividual(ItemStack itemstack);
+	public abstract IIndividual getIndividual(ItemStack itemstack);
 
 	protected abstract IAlleleSpecies getSpecies(ItemStack itemStack);
 

src/main/java/forestry/core/network/PacketIds.java

@@ -1,62 +1,63 @@
-/*******************************************************************************
- * 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.network;
-
-/**
- * Valid ids: 0 - 127
- */
-public class PacketIds {
-
-	public static final int TILE_FORESTRY_UPDATE = 0;
-	public static final int TILE_UPDATE = 1;
-	public static final int TILE_DESCRIPTION = 2;
-	public static final int IINVENTORY_STACK = 3;
-	public static final int FX_SIGNAL = 4;
-	public static final int TILE_NBT = 5;
-
-	public static final int HABITAT_BIOME_POINTER = 20;
-
-	public static final int GUI_SELECTION_CHANGE = 30;
-	public static final int IMPRINT_SELECTION_GET = 31;
-	public static final int GUI_SELECTION = 32;
-
-	public static final int PIPETTE_CLICK = 40;
-
-	public static final int ACCESS_SWITCH = 50;
-
-	public static final int GENOME_TRACKER_UPDATE = 60;
-	public static final int GAME_TOKEN_SET = 61;
-
-	public static final int CHIPSET_CLICK = 70;
-	public static final int SOLDERING_IRON_CLICK = 71;
-	public static final int SOCKET_UPDATE = 72;
-
-	public static final int LETTER_RECIPIENT = 80;
-	public static final int LETTER_TEXT = 81;
-	public static final int TRADING_ADDRESS_SET = 82;
-	public static final int LETTER_INFO = 83;
-	public static final int POBOX_INFO = 85;
-	public static final int POBOX_INFO_REQUEST = 86;
-
-	public static final int LEAF_UPDATE = 90;
-	
-	public static final int GUI_INTEGER = 92;
-	
-	// Propolis pipe
-	public static final int PROP_SEND_FILTER_SET = 100;
-	public static final int PROP_REQUEST_FILTER_SET = 101;
-	public static final int PROP_SEND_FILTER_CHANGE_GENOME = 102;
-	public static final int PROP_SEND_FILTER_CHANGE_TYPE = 103;
-	
-	
-	
-
-}
+/*******************************************************************************
+ * 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.network;
+
+/**
+ * Valid ids: 0 - 127
+ */
+public class PacketIds {
+
+	public static final int TILE_FORESTRY_UPDATE = 0;
+	public static final int TILE_UPDATE = 1;
+	public static final int TILE_DESCRIPTION = 2;
+	public static final int IINVENTORY_STACK = 3;
+	public static final int FX_SIGNAL = 4;
+	public static final int TILE_NBT = 5;
+
+	public static final int HABITAT_BIOME_POINTER = 20;
+
+	public static final int GUI_SELECTION_CHANGE = 30;
+	public static final int IMPRINT_SELECTION_GET = 31;
+	public static final int GUI_SELECTION = 32;
+
+	public static final int PIPETTE_CLICK = 40;
+
+	public static final int ACCESS_SWITCH = 50;
+
+	public static final int GENOME_TRACKER_UPDATE = 60;
+	public static final int GAME_TOKEN_SET = 61;
+
+	public static final int CHIPSET_CLICK = 70;
+	public static final int SOLDERING_IRON_CLICK = 71;
+	public static final int SOCKET_UPDATE = 72;
+
+	public static final int LETTER_RECIPIENT = 80;
+	public static final int LETTER_TEXT = 81;
+	public static final int TRADING_ADDRESS_SET = 82;
+	public static final int LETTER_INFO = 83;
+	public static final int POBOX_INFO = 85;
+	public static final int POBOX_INFO_REQUEST = 86;
+
+	public static final int LEAF_UPDATE = 90;
+	public static final int RIPENING_UPDATE = 91;
+	
+	public static final int GUI_INTEGER = 92;
+	
+	// Propolis pipe
+	public static final int PROP_SEND_FILTER_SET = 100;
+	public static final int PROP_REQUEST_FILTER_SET = 101;
+	public static final int PROP_SEND_FILTER_CHANGE_GENOME = 102;
+	public static final int PROP_SEND_FILTER_CHANGE_TYPE = 103;
+	
+	
+	
+
+}

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

@@ -18,6 +18,7 @@ import net.minecraft.block.Block;
 import net.minecraft.block.material.Material;
 import net.minecraft.entity.player.EntityPlayer;
 import net.minecraft.init.Blocks;
+import net.minecraft.item.Item;
 import net.minecraft.item.ItemStack;
 import net.minecraft.tileentity.TileEntity;
 import net.minecraft.world.World;
@@ -30,6 +31,7 @@ import forestry.api.core.IArmorNaturalist;
 import forestry.api.genetics.AlleleManager;
 import forestry.api.genetics.IIndividual;
 import forestry.api.genetics.IPollinatable;
+import forestry.core.genetics.ItemGE;
 import forestry.plugins.PluginArboriculture;
 
 public class GeneticsUtil {
@@ -65,7 +67,7 @@ public class GeneticsUtil {
 			return (IPollinatable) tile;
 		}
 
-		IIndividual pollen = getErsatzPollen(world, x, y, z);
+		ITree pollen = getErsatzPollen(world, x, y, z);
 		if (pollen != null) {
 			PluginArboriculture.treeInterface.setLeaves(world, pollen, owner, x, y, z);
 			return (IPollinatable) world.getTileEntity(x, y, z);
@@ -74,7 +76,7 @@ public class GeneticsUtil {
 		return null;
 	}
 
-	public static IIndividual getErsatzPollen(World world, final int x, final int y, final int z) {
+	public static ITree getErsatzPollen(World world, final int x, final int y, final int z) {
 		Block block = world.getBlock(x, y, z);
 		if (!isErsatzMaterial(block))
 			return null;
@@ -89,35 +91,33 @@ public class GeneticsUtil {
 			}
 			meta %= 3;
 		}
-
-		// Find the matching ersatz genome
-		for (ItemStack ersatzSpecimen : AlleleManager.ersatzSpecimen.keySet()) {
-			if (StackUtils.equals(block, meta, ersatzSpecimen)) {
-				return AlleleManager.ersatzSpecimen.get(ersatzSpecimen).copy();
-			}
-		}
+		ItemStack itemStack = new ItemStack(block, meta);
+		IIndividual tree = getGeneticEquivalent(itemStack);
+		if (tree instanceof ITree)
+			return (ITree) tree;
 
 		return null;
 	}
 
-	public static ItemStack convertSaplingToGeneticEquivalent(ItemStack foreign) {
-
-		ItemStack ersatz = null;
-		ITree tree = null;
+	public static IIndividual getGeneticEquivalent(ItemStack itemStack) {
+		Item item = itemStack.getItem();
+		if (item instanceof ItemGE)
+			return ((ItemGE) item).getIndividual(itemStack);
 
 		for (Map.Entry<ItemStack, IIndividual> entry : AlleleManager.ersatzSaplings.entrySet()) {
-			if (entry.getKey().getItem() != foreign.getItem())
-				continue;
-			if (entry.getKey().getItemDamage() != foreign.getItemDamage())
-				continue;
-
-			if (entry.getValue() instanceof ITree)
-				tree = (ITree) entry.getValue();
-
-			ersatz = PluginArboriculture.treeInterface.getMemberStack(tree, EnumGermlingType.SAPLING.ordinal());
-			ersatz.stackSize = foreign.stackSize;
+			if (StackUtils.isIdenticalItem(itemStack, entry.getKey()))
+				return entry.getValue().copy();
 		}
+		return null;
+	}
 
+	public static ItemStack convertSaplingToGeneticEquivalent(ItemStack foreign) {
+		IIndividual tree = getGeneticEquivalent(foreign);
+		if (!(tree instanceof ITree))
+			return null;
+
+		ItemStack ersatz = PluginArboriculture.treeInterface.getMemberStack(tree, EnumGermlingType.SAPLING.ordinal());
+		ersatz.stackSize = foreign.stackSize;
 		return ersatz;
 	}
 }

src/main/java/forestry/core/worldgen/BlockType.java

@@ -33,8 +33,6 @@ public class BlockType {
 
 	public void setBlock(World world, ITreeGenData tree, int x, int y, int z) {
 		world.setBlock(x, y, z, block, meta, Defaults.FLAG_BLOCK_SYNCH);
-		if (world.getTileEntity(x, y, z) != null)
-			world.removeTileEntity(x, y, z);
 	}
 	
 	public int getMeta() {

src/main/java/forestry/farming/logic/FarmableGE.java

@@ -36,7 +36,7 @@ public class FarmableGE implements IFarmable {
 	public ICrop getCropAt(World world, int x, int y, int z) {
 		Block block = world.getBlock(x, y, z);
 
-		if (block.isAir(world, x, y, z) || !block.isWood(world, x, y, z))
+		if (!block.isWood(world, x, y, z))
 			return null;
 
 		return new CropBlock(world, block, world.getBlockMetadata(x, y, z), new Vect(x, y, z));

src/main/java/forestry/farming/logic/FarmableVanillaSapling.java

@@ -10,17 +10,17 @@
  ******************************************************************************/
 package forestry.farming.logic;
 
-import forestry.api.arboriculture.ITree;
-import forestry.api.genetics.AlleleManager;
-import forestry.api.genetics.IIndividual;
-import forestry.plugins.PluginArboriculture;
-import java.util.Map;
 import net.minecraft.entity.player.EntityPlayer;
 import net.minecraft.init.Blocks;
 import net.minecraft.init.Items;
 import net.minecraft.item.ItemStack;
 import net.minecraft.world.World;
 
+import forestry.api.arboriculture.ITree;
+import forestry.api.genetics.IIndividual;
+import forestry.core.utils.GeneticsUtil;
+import forestry.plugins.PluginArboriculture;
+
 public class FarmableVanillaSapling extends FarmableGenericSapling {
 
 	public FarmableVanillaSapling() {
@@ -29,17 +29,11 @@ public class FarmableVanillaSapling extends FarmableGenericSapling {
 
 	@Override
 	public boolean plantSaplingAt(EntityPlayer player, ItemStack germling, World world, int x, int y, int z) {
-		ITree tree = null;
-		for (Map.Entry<ItemStack, IIndividual> entry : AlleleManager.ersatzSaplings.entrySet())
-			if (entry.getKey().isItemEqual(germling) && entry.getValue() instanceof ITree) {
-				tree = (ITree) entry.getValue();
-				break;
-			}
-
-		if (tree == null)
+		IIndividual tree = GeneticsUtil.getGeneticEquivalent(germling);
+		if (!(tree instanceof ITree))
 			return false;
 
-		return PluginArboriculture.treeInterface.plantSapling(world, tree, player.getGameProfile(), x, y, z);
+		return PluginArboriculture.treeInterface.plantSapling(world, (ITree)tree, player.getGameProfile(), x, y, z);
 	}
 
 }

src/main/java/forestry/lepidopterology/items/ItemButterflyGE.java

@@ -60,7 +60,7 @@ public class ItemButterflyGE extends ItemGE {
 	}
 
 	@Override
-	protected IIndividual getIndividual(ItemStack itemstack) {
+	public IButterfly getIndividual(ItemStack itemstack) {
 		return PluginLepidopterology.butterflyInterface.getMember(itemstack);
 	}