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A pure Java HDF5 library
There is a newer version: 0.9.4
/*
 * This file is part of jHDF. A pure Java library for accessing HDF5 files.
 *
 * https://jhdf.io
 *
 * Copyright (c) 2025 James Mudd
 *
 * MIT License see 'LICENSE' file
 */
package io.jhdf.btree;

import io.jhdf.Utils;
import io.jhdf.exceptions.HdfException;
import io.jhdf.storage.HdfBackingStorage;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.nio.ByteBuffer;
import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.List;

/**
 * Class to represent V1 B-trees
 *
 * 
 * Format
 * Spec
 * 
 *
 * @author James Mudd
 */
public abstract class BTreeV1 {
	private static final Logger logger = LoggerFactory.getLogger(BTreeV1.class);

	private static final byte[] BTREE_NODE_V1_SIGNATURE = "TREE".getBytes(StandardCharsets.US_ASCII);
	private static final int HEADER_BYTES = 6;

	/**
	 * The location of this B tree in the file
	 */
	private final long address;
	protected final int entriesUsed;
	private final long leftSiblingAddress;
	private final long rightSiblingAddress;

	public static BTreeV1Group createGroupBTree(HdfBackingStorage hdfBackingStorage, long address) {
		ByteBuffer header = readHeaderAndValidateSignature(hdfBackingStorage, address);

		final byte nodeType = header.get();
		if (nodeType != 0) {
			throw new HdfException("B tree type is not group. Type is: " + nodeType);
		}

		final byte nodeLevel = header.get();

		if (nodeLevel > 0) {
			return new BTreeV1Group.BTreeV1GroupNonLeafNode(hdfBackingStorage, address);
		} else {
			return new BTreeV1Group.BTreeV1GroupLeafNode(hdfBackingStorage, address);
		}

	}

	public static BTreeV1Data createDataBTree(HdfBackingStorage hdfBackingStorage, long address, int dataDimensions) {
		ByteBuffer header = readHeaderAndValidateSignature(hdfBackingStorage, address);

		final byte nodeType = header.get();
		if (nodeType != 1) {
			throw new HdfException("B tree type is not data. Type is: " + nodeType);
		}

		final byte nodeLevel = header.get();

		if (nodeLevel > 0) {
			return new BTreeV1Data.BTreeV1DataNonLeafNode(hdfBackingStorage, address, dataDimensions);
		} else {
			return new BTreeV1Data.BTreeV1DataLeafNode(hdfBackingStorage, address, dataDimensions);
		}
	}

	public static ByteBuffer readHeaderAndValidateSignature(HdfBackingStorage fc, long address) {
		ByteBuffer header = fc.readBufferFromAddress(address, HEADER_BYTES);

		// Verify signature
		byte[] formatSignatureByte = new byte[4];
		header.get(formatSignatureByte, 0, formatSignatureByte.length);
		if (!Arrays.equals(BTREE_NODE_V1_SIGNATURE, formatSignatureByte)) {
			throw new HdfException("B tree V1 node signature not matched");
		}
		return header;
	}

	/* package */ BTreeV1(HdfBackingStorage hdfBackingStorage, long address) {
		this.address = address;

		int headerSize = 8 * hdfBackingStorage.getSizeOfOffsets();
		ByteBuffer header = hdfBackingStorage.readBufferFromAddress(address + 6, headerSize);

		entriesUsed = Utils.readBytesAsUnsignedInt(header, 2);
		logger.trace("Entries = {}", entriesUsed);

		leftSiblingAddress = Utils.readBytesAsUnsignedLong(header, hdfBackingStorage.getSizeOfOffsets());
		logger.trace("left address = {}", leftSiblingAddress);

		rightSiblingAddress = Utils.readBytesAsUnsignedLong(header, hdfBackingStorage.getSizeOfOffsets());
		logger.trace("right address = {}", rightSiblingAddress);

	}

	public int getEntriesUsed() {
		return entriesUsed;
	}

	public long getLeftSiblingAddress() {
		return leftSiblingAddress;
	}

	public long getRightSiblingAddress() {
		return rightSiblingAddress;
	}

	public long getAddress() {
		return address;
	}

	public abstract List getChildAddresses();

}