add javadoc to mca library and make some functions public

.gitignore

@@ -81,4 +81,7 @@ local.properties
 doc/
 
 # ignore out
-out/
+out/
+
+# ignore patches
+*.patch

src/main/java/net/querz/nbt/mca/Chunk.java

@@ -42,6 +42,10 @@ public class Chunk {
 		this.lastMCAUpdate = lastMCAUpdate;
 	}
 
+	/**
+	 * Create a new chunk based on raw base data from a region file.
+	 * @param data The raw base data to be used.
+	 */
 	public Chunk(CompoundTag data) {
 		this.data = data;
 		initReferences();
@@ -86,6 +90,14 @@ private void initReferences() {
 		}
 	}
 
+	/**
+	 * Serializes this chunk to a <code>RandomAccessFile</code>.
+	 * @param raf The RandomAccessFile to be written to.
+	 * @param xPos The x-coordinate of the chunk.
+	 * @param zPos The z-coodrinate of the chunk.
+	 * @return The amount of bytes written to the RandomAccessFile.
+	 * @throws IOException When something went wrong during writing.
+	 */
 	public int serialize(RandomAccessFile raf, int xPos, int zPos) throws IOException {
 		ByteArrayOutputStream baos = new ByteArrayOutputStream(4096);
 		try (DataOutputStream nbtOut = new DataOutputStream(new BufferedOutputStream(CompressionType.ZLIB.compress(baos)))) {
@@ -98,6 +110,11 @@ public int serialize(RandomAccessFile raf, int xPos, int zPos) throws IOExceptio
 		return rawData.length + 5;
 	}
 
+	/**
+	 * Reads chunk data from a RandomAccessFile. The RandomAccessFile must already be at the correct position.
+	 * @param raf The RandomAccessFile to read the chunk data from.
+	 * @throws IOException When something went wrong during reading.
+	 */
 	public void deserialize(RandomAccessFile raf) throws IOException {
 		byte compressionTypeByte = raf.readByte();
 		CompressionType compressionType = CompressionType.getFromID(compressionTypeByte);
@@ -114,13 +131,28 @@ public void deserialize(RandomAccessFile raf) throws IOException {
 		}
 	}
 
+	/**
+	 * Fetches a biome id at a specific block column in this chunk.
+	 * The coordinates can be absolute coordinates or relative to the region or chunk.
+	 * @param blockX The x-coordinate of the block column.
+	 * @param blockZ The z-coordinate of the block column.
+	 * @return The biome id or -1 if the biomes are not correctly initialized.
+	 */
 	public int getBiomeAt(int blockX, int blockZ) {
 		if (biomes == null || biomes.length != 256) {
 			return -1;
 		}
 		return biomes[getBlockIndex(blockX, blockZ)];
 	}
 
+	/**
+	 * Sets a biome id at a specific block column.
+	 * The coordinates can be absolute coordinates or relative to the region or chunk.
+	 * @param blockX The x-coordinate of the block column.
+	 * @param blockZ The z-coordinate of the block column.
+	 * @param biomeID The biome id to be set.
+	 *                When set to a negative number, Minecraft will replace it with the block column's default biome.
+	 */
 	public void setBiomeAt(int blockX, int blockZ, int biomeID) {
 		if (biomes == null || biomes.length != 256) {
 			biomes = new int[256];
@@ -131,6 +163,14 @@ public void setBiomeAt(int blockX, int blockZ, int biomeID) {
 		biomes[getBlockIndex(blockX, blockZ)] = biomeID;
 	}
 
+	/**
+	 * Fetches the block state at a specific block location in this chunk.
+	 * The block coordinate can be absolute or relative to the region or chunk.
+	 * @param blockX The x-coordinate of the block.
+	 * @param blockY The y-coordinate of the block.
+	 * @param blockZ The z-coordinate of the block.
+	 * @return The block state or null if a section at the location does not exist.
+	 */
 	public CompoundTag getBlockStateAt(int blockX, int blockY, int blockZ) {
 		Section section = sections[MCAUtil.blockToChunk(blockY)];
 		if (section == null) {
@@ -139,6 +179,17 @@ public CompoundTag getBlockStateAt(int blockX, int blockY, int blockZ) {
 		return section.getBlockStateAt(blockX, blockY, blockZ);
 	}
 
+	/**
+	 * Sets a block state at a specific location.
+	 * The block coordinates can be absolute or relative to the region or chunk.
+	 * @param blockX The x-coordinate of the block.
+	 * @param blockY The y-coordinate of the block.
+	 * @param blockZ The z-coordinate of the block.
+	 * @param state The block state to be set.
+	 * @param cleanup When <code>true</code>, it will cleanup all palettes of this chunk.
+	 *                This option should only be used moderately to avoid unnecessary recalculation of the palette indices.
+	 *                Recalculating the Palette should only be executed once right before saving the Chunk to file.
+	 */
 	public void setBlockStateAt(int blockX, int blockY, int blockZ, CompoundTag state, boolean cleanup) {
 		int sectionIndex = MCAUtil.blockToChunk(blockY);
 		Section section = sections[sectionIndex];
@@ -148,149 +199,281 @@ public void setBlockStateAt(int blockX, int blockY, int blockZ, CompoundTag stat
 		section.setBlockStateAt(blockX, blockY, blockZ, state, cleanup);
 	}
 
+	/**
+	 * @return The DataVersion of this chunk.
+	 */
 	public int getDataVersion() {
 		return dataVersion;
 	}
 
+	/**
+	 * Sets the DataVersion of this chunk. This does not check if the data of this chunk conforms
+	 * to that DataVersion, that is the responsibility of the developer.
+	 * @param dataVersion The DataVersion to be set.
+	 */
 	public void setDataVersion(int dataVersion) {
 		this.dataVersion = dataVersion;
 	}
 
+	/**
+	 * @return The timestamp when this region file was last updated in seconds since 1970-01-01.
+	 */
 	public int getLastMCAUpdate() {
 		return lastMCAUpdate;
 	}
 
+	/**
+	 * Sets the timestamp when this region file was last updated in seconds since 1970-01-01.
+	 * @param lastMCAUpdate The time in seconds since 1970-01-01.
+	 */
 	public void setLastMCAUpdate(int lastMCAUpdate) {
 		this.lastMCAUpdate = lastMCAUpdate;
 	}
 
+	/**
+	 * @return The generation station of this chunk.
+	 */
 	public String getStatus() {
 		return status;
 	}
 
+	/**
+	 * Sets the generation status of this chunk.
+	 * @param status The generation status of this chunk.
+	 */
 	public void setStatus(String status) {
 		this.status = status;
 	}
 
+	/**
+	 * Fetches the section at the given y-coordinate.
+	 * @param sectionY The y-coordinate of the section in this chunk ranging from 0 to 15.
+	 * @return The Section.
+	 */
 	public Section getSection(int sectionY) {
 		return sections[sectionY];
 	}
 
+	/**
+	 * Sets a section at a givesn y-coordinate
+	 * @param sectionY The y-coordinate of the section in this chunk ranging from 0 to 15.
+	 * @param section The section to be set.
+	 */
 	public void setSection(int sectionY, Section section) {
 		sections[sectionY] = section;
 	}
 
+	/**
+	 * @return The timestamp when this chunk was last updated as a UNIX timestamp.
+	 */
 	public long getLastUpdate() {
 		return lastUpdate;
 	}
 
+	/**
+	 * Sets the time when this chunk was last updated as a UNIX timestamp.
+	 * @param lastUpdate The UNIX timestamp.
+	 */
 	public void setLastUpdate(long lastUpdate) {
 		this.lastUpdate = lastUpdate;
 	}
 
+	/**
+	 * @return The cumulative amount of time players have spent in this chunk in ticks.
+	 */
 	public long getInhabitedTime() {
 		return inhabitedTime;
 	}
 
+	/**
+	 * Sets the cumulative amount of time players have spent in this chunk in ticks.
+	 * @param inhabitedTime The time in ticks.
+	 */
 	public void setInhabitedTime(long inhabitedTime) {
 		this.inhabitedTime = inhabitedTime;
 	}
 
+	/**
+	 * @return A matrix of biome IDs for all block columns in this chunk.
+	 */
 	public int[] getBiomes() {
 		return biomes;
 	}
 
+	/**
+	 * Sets the biome IDs for this chunk.
+	 * @param biomes The biome ID matrix of this chunk. Must have a length of <code>256</code>.
+	 * @throws IllegalArgumentException When the biome matrix does not have a length of <code>256</code>
+	 *                                  or is <code>null</code>
+	 */
 	public void setBiomes(int[] biomes) {
 		if (biomes != null && biomes.length != 256) {
 			throw new IllegalArgumentException("biomes array must have a length of 256");
 		}
 		this.biomes = biomes;
 	}
 
+	/**
+	 * @return The height maps of this chunk.
+	 */
 	public CompoundTag getHeightMaps() {
 		return heightMaps;
 	}
 
+	/**
+	 * Sets the height maps of this chunk.
+	 * @param heightMaps The height maps.
+	 */
 	public void setHeightMaps(CompoundTag heightMaps) {
 		this.heightMaps = heightMaps;
 	}
 
+	/**
+	 * @return The carving masks of this chunk.
+	 */
 	public CompoundTag getCarvingMasks() {
 		return carvingMasks;
 	}
 
+	/**
+	 * Sets the carving masks of this chunk.
+	 * @param carvingMasks The carving masks.
+	 */
 	public void setCarvingMasks(CompoundTag carvingMasks) {
 		this.carvingMasks = carvingMasks;
 	}
 
+	/**
+	 * @return The entities of this chunk.
+	 */
 	public ListTag<CompoundTag> getEntities() {
 		return entities;
 	}
 
+	/**
+	 * Sets the entities of this chunk.
+	 * @param entities The entities.
+	 */
 	public void setEntities(ListTag<CompoundTag> entities) {
 		this.entities = entities;
 	}
 
+	/**
+	 * @return The tile entities of this chunk.
+	 */
 	public ListTag<CompoundTag> getTileEntities() {
 		return tileEntities;
 	}
 
+	/**
+	 * Sets the tile entities of this chunk.
+	 * @param tileEntities The tile entities of this chunk.
+	 */
 	public void setTileEntities(ListTag<CompoundTag> tileEntities) {
 		this.tileEntities = tileEntities;
 	}
 
+	/**
+	 * @return The tile ticks of this chunk.
+	 */
 	public ListTag<CompoundTag> getTileTicks() {
 		return tileTicks;
 	}
 
+	/**
+	 * Sets the tile ticks of this chunk.
+	 * @param tileTicks Thee tile ticks.
+	 */
 	public void setTileTicks(ListTag<CompoundTag> tileTicks) {
 		this.tileTicks = tileTicks;
 	}
 
+	/**
+	 * @return The liquid ticks of this chunk.
+	 */
 	public ListTag<CompoundTag> getLiquidTicks() {
 		return liquidTicks;
 	}
 
+	/**
+	 * Sets the liquid ticks of this chunk.
+	 * @param liquidTicks The liquid ticks.
+	 */
 	public void setLiquidTicks(ListTag<CompoundTag> liquidTicks) {
 		this.liquidTicks = liquidTicks;
 	}
 
+	/**
+	 * @return The light sources in this chunk.
+	 */
 	public ListTag<ListTag<?>> getLights() {
 		return lights;
 	}
 
+	/**
+	 * Sets the light sources in this chunk.
+	 * @param lights The light sources.
+	 */
 	public void setLights(ListTag<ListTag<?>> lights) {
 		this.lights = lights;
 	}
 
+	/**
+	 * @return THe liquids to be ticked in this chunk.
+	 */
 	public ListTag<ListTag<?>> getLiquidsToBeTicked() {
 		return liquidsToBeTicked;
 	}
 
+	/**
+	 * Sets the liquids to be ticked in this chunk.
+	 * @param liquidsToBeTicked The liquids to be ticked.
+	 */
 	public void setLiquidsToBeTicked(ListTag<ListTag<?>> liquidsToBeTicked) {
 		this.liquidsToBeTicked = liquidsToBeTicked;
 	}
 
+	/**
+	 * @return Stuff to be ticked in this chunk.
+	 */
 	public ListTag<ListTag<?>> getToBeTicked() {
 		return toBeTicked;
 	}
 
+	/**
+	 * Sets stuff to be ticked in this chunk.
+	 * @param toBeTicked The stuff to be ticked.
+	 */
 	public void setToBeTicked(ListTag<ListTag<?>> toBeTicked) {
 		this.toBeTicked = toBeTicked;
 	}
 
+	/**
+	 * @return Things that are in post processing in this chunk.
+	 */
 	public ListTag<ListTag<?>> getPostProcessing() {
 		return postProcessing;
 	}
 
+	/**
+	 * Sets things to be post processed in this chunk.
+	 * @param postProcessing The things to be post processed.
+	 */
 	public void setPostProcessing(ListTag<ListTag<?>> postProcessing) {
 		this.postProcessing = postProcessing;
 	}
 
+	/**
+	 * @return Data about structures in this chunk.
+	 */
 	public CompoundTag getStructures() {
 		return structures;
 	}
 
+	/**
+	 * Sets data about structures in this chunk.
+	 * @param structures The data about structures.
+	 */
 	public void setStructures(CompoundTag structures) {
 		this.structures = structures;
 	}