Merge pull request #258 from jamesmudd/hdfFc-rename

Rename hdfFc → hdfBackingStorage where appropriate

jhdf/src/main/java/io/jhdf/AbstractNode.java

@@ -56,14 +56,14 @@ protected Map<String, Attribute> initialize() throws ConcurrentException {
 
 				if (attributeInfoMessage.getFractalHeapAddress() != Constants.UNDEFINED_ADDRESS) {
 					// Create the heap and btree
-					FractalHeap fractalHeap = new FractalHeap(hdfFc, attributeInfoMessage.getFractalHeapAddress());
-					BTreeV2<AttributeNameForIndexedAttributesRecord> btree = new BTreeV2<>(hdfFc,
+					FractalHeap fractalHeap = new FractalHeap(hdfBackingStorage, attributeInfoMessage.getFractalHeapAddress());
+					BTreeV2<AttributeNameForIndexedAttributesRecord> btree = new BTreeV2<>(hdfBackingStorage,
 							attributeInfoMessage.getAttributeNameBTreeAddress());
 
 					// Read the attribute messages from the btree+heap
 					for (AttributeNameForIndexedAttributesRecord attributeRecord : btree.getRecords()) {
 						ByteBuffer bb = fractalHeap.getId(attributeRecord.getHeapId());
-						AttributeMessage attributeMessage = new AttributeMessage(bb, hdfFc,
+						AttributeMessage attributeMessage = new AttributeMessage(bb, hdfBackingStorage,
 								attributeRecord.getFlags());
 						logger.trace("Read attribute message '{}'", attributeMessage);
 						attributeMessages.add(attributeMessage);
@@ -77,25 +77,25 @@ protected Map<String, Attribute> initialize() throws ConcurrentException {
 			return attributeMessages.stream()
 					.collect(
 							toMap(AttributeMessage::getName,
-									message -> new AttributeImpl(hdfFc, AbstractNode.this, message)));
+									message -> new AttributeImpl(hdfBackingStorage, AbstractNode.this, message)));
 		}
 	}
 
-	private final HdfBackingStorage hdfFc;
+	private final HdfBackingStorage hdfBackingStorage;
 	protected final long address;
 	protected final String name;
 	protected final Group parent;
 	protected final LazyInitializer<ObjectHeader> header;
 	protected final AttributesLazyInitializer attributes;
 
-	protected AbstractNode(HdfBackingStorage hdfFc, long address, String name, Group parent) {
-		this.hdfFc = hdfFc;
+	protected AbstractNode(HdfBackingStorage hdfBackingStorage, long address, String name, Group parent) {
+		this.hdfBackingStorage = hdfBackingStorage;
 		this.address = address;
 		this.name = name;
 		this.parent = parent;
 
 		try {
-			header = ObjectHeader.lazyReadObjectHeader(hdfFc, address);
+			header = ObjectHeader.lazyReadObjectHeader(hdfBackingStorage, address);
 
 			// Attributes
 			attributes = new AttributesLazyInitializer(header);

jhdf/src/main/java/io/jhdf/AttributeImpl.java

@@ -25,13 +25,13 @@
 public class AttributeImpl implements Attribute {
 	private static final Logger logger = LoggerFactory.getLogger(AttributeImpl.class);
 
-	private final HdfBackingStorage hdfFc;
+	private final HdfBackingStorage hdfBackingStorage;
 	private final Node node;
 	private final String name;
 	private final AttributeMessage message;
 
-	public AttributeImpl(HdfBackingStorage hdfFc, Node node, AttributeMessage message) {
-		this.hdfFc = hdfFc;
+	public AttributeImpl(HdfBackingStorage hdfBackingStorage, Node node, AttributeMessage message) {
+		this.hdfBackingStorage = hdfBackingStorage;
 		this.node = node;
 		this.name = message.getName();
 		this.message = message;
@@ -70,7 +70,7 @@ public Object getData() {
 		}
 		DataType type = message.getDataType();
 		ByteBuffer bb = message.getDataBuffer();
-		return DatasetReader.readDataset(type, bb, getDimensions(), hdfFc);
+		return DatasetReader.readDataset(type, bb, getDimensions(), hdfBackingStorage);
 	}
 
 	@Override

jhdf/src/main/java/io/jhdf/CommittedDatatype.java

@@ -19,8 +19,8 @@
 
 public class CommittedDatatype extends AbstractNode {
 
-	public CommittedDatatype(HdfBackingStorage hdfFc, long address, String name, Group parent) {
-		super(hdfFc, address, name, parent);
+	public CommittedDatatype(HdfBackingStorage hdfBackingStorage, long address, String name, Group parent) {
+		super(hdfBackingStorage, address, name, parent);
 	}
 
 	@Override

jhdf/src/main/java/io/jhdf/FractalHeap.java

@@ -59,7 +59,7 @@ public class FractalHeap {
 	private static final BigInteger TWO = BigInteger.valueOf(2L);
 
 	private final long address;
-	private final HdfBackingStorage hdfFc;
+	private final HdfBackingStorage hdfBackingStorage;
 	private final Superblock sb;
 
 	private final int maxDirectBlockSize;
@@ -95,15 +95,15 @@ public class FractalHeap {
 	private final int bytesToStoreOffset;
 	private final int bytesToStoreLength;
 
-	public FractalHeap(HdfBackingStorage hdfFc, long address) {
-		this.hdfFc = hdfFc;
-		this.sb = hdfFc.getSuperblock();
+	public FractalHeap(HdfBackingStorage hdfBackingStorage, long address) {
+		this.hdfBackingStorage = hdfBackingStorage;
+		this.sb = hdfBackingStorage.getSuperblock();
 		this.address = address;
 
 		final int headerSize = 4 + 1 + 2 + 2 + 1 + 4 + 12 * sb.getSizeOfLengths() + 3 * sb.getSizeOfOffsets() + 2
 				+ 2 + 2 + 2 + 4;
 
-		ByteBuffer bb = hdfFc.readBufferFromAddress(address, headerSize);
+		ByteBuffer bb = hdfBackingStorage.readBufferFromAddress(address, headerSize);
 
 		byte[] formatSignatureBytes = new byte[4];
 		bb.get(formatSignatureBytes, 0, formatSignatureBytes.length);
@@ -228,15 +228,15 @@ public ByteBuffer getId(ByteBuffer buffer) {
 			}
 
 			BTreeV2<HugeFractalHeapObjectUnfilteredRecord> hugeObjectBTree =
-			    new BTreeV2<>(this.hdfFc, this.bTreeAddressOfHugeObjects);
+			    new BTreeV2<>(this.hdfBackingStorage, this.bTreeAddressOfHugeObjects);
 
 			if (hugeObjectBTree.getRecords().size() != 1) {
 			    throw new UnsupportedHdfException("Only Huge objects BTrees with 1 record are currently supported");
 			}
 
 			HugeFractalHeapObjectUnfilteredRecord ho = hugeObjectBTree.getRecords().get(0);
 
-			return this.hdfFc.readBufferFromAddress(ho.getAddress(), (int) ho.getLength());
+			return this.hdfBackingStorage.readBufferFromAddress(ho.getAddress(), (int) ho.getLength());
 		case 2: // Tiny objects
 			throw new UnsupportedHdfException("Tiny objects are currently not supported");
 		default:
@@ -252,7 +252,7 @@ private IndirectBlock(long address) {
 			final int headerSize = 4 + 1 + sb.getSizeOfOffsets() + bytesToStoreOffset
 					+ currentRowsInRootIndirectBlock * tableWidth * getRowSize() + 4;
 
-			ByteBuffer bb = hdfFc.readBufferFromAddress(address, headerSize);
+			ByteBuffer bb = hdfBackingStorage.readBufferFromAddress(address, headerSize);
 
 			byte[] formatSignatureBytes = new byte[4];
 			bb.get(formatSignatureBytes, 0, formatSignatureBytes.length);
@@ -319,7 +319,7 @@ private DirectBlock(long address) {
 
 			final int headerSize = 4 + 1 + sb.getSizeOfOffsets() + bytesToStoreOffset + 4;
 
-			ByteBuffer bb = hdfFc.readBufferFromAddress(address, headerSize);
+			ByteBuffer bb = hdfBackingStorage.readBufferFromAddress(address, headerSize);
 
 			byte[] formatSignatureBytes = new byte[4];
 			bb.get(formatSignatureBytes, 0, formatSignatureBytes.length);
@@ -342,7 +342,7 @@ private DirectBlock(long address) {
 
 			blockOffset = readBytesAsUnsignedLong(bb, bytesToStoreOffset);
 
-			data = hdfFc.map(address, getSizeOfDirectBlock(blockIndex));
+			data = hdfBackingStorage.map(address, getSizeOfDirectBlock(blockIndex));
 
 			if (checksumPresent()) {
 				int storedChecksum = bb.getInt();

jhdf/src/main/java/io/jhdf/GlobalHeap.java

@@ -26,19 +26,19 @@ public class GlobalHeap {
 
 	private static final byte[] GLOBAL_HEAP_SIGNATURE = "GCOL".getBytes(StandardCharsets.US_ASCII);
 
-	private final HdfBackingStorage hdfFc;
+	private final HdfBackingStorage hdfBackingStorage;
 	private final long address;
 
 	private final Map<Integer, GlobalHeapObject> objects = new HashMap<>();
 
-	public GlobalHeap(HdfBackingStorage hdfFc, long address) {
-		this.hdfFc = hdfFc;
+	public GlobalHeap(HdfBackingStorage hdfBackingStorage, long address) {
+		this.hdfBackingStorage = hdfBackingStorage;
 		this.address = address;
 
 		try {
-			int headerSize = 4 + 1 + 3 + hdfFc.getSizeOfLengths();
+			int headerSize = 4 + 1 + 3 + hdfBackingStorage.getSizeOfLengths();
 
-			ByteBuffer bb = hdfFc.readBufferFromAddress(address, headerSize);
+			ByteBuffer bb = hdfBackingStorage.readBufferFromAddress(address, headerSize);
 
 			byte[] signatureBytes = new byte[4];
 			bb.get(signatureBytes, 0, signatureBytes.length);
@@ -56,12 +56,12 @@ public GlobalHeap(HdfBackingStorage hdfFc, long address) {
 
 			bb.position(8); // Skip past 3 reserved bytes
 
-			int collectionSize = readBytesAsUnsignedInt(bb, hdfFc.getSizeOfLengths());
+			int collectionSize = readBytesAsUnsignedInt(bb, hdfBackingStorage.getSizeOfLengths());
 
 			// Collection size contains size of whole collection, so substract already read bytes
-			int remainingCollectionSize = collectionSize - 8 - hdfFc.getSizeOfLengths();
+			int remainingCollectionSize = collectionSize - 8 - hdfBackingStorage.getSizeOfLengths();
 			// Now start reading the heap into memory
-			bb = hdfFc.readBufferFromAddress(address + headerSize, remainingCollectionSize);
+			bb = hdfBackingStorage.readBufferFromAddress(address + headerSize, remainingCollectionSize);
 
 			// minimal global heap object is 16 bytes
 			while (bb.remaining() >= 16) {
@@ -94,10 +94,10 @@ private GlobalHeapObject(GlobalHeap globalHeap, ByteBuffer bb) {
 			index = readBytesAsUnsignedInt(bb, 2);
 			referenceCount = readBytesAsUnsignedInt(bb, 2);
 			bb.position(bb.position() + 4); // Skip 4 reserved bytes
-			int size = readBytesAsUnsignedInt(bb, globalHeap.hdfFc.getSizeOfOffsets());
+			int size = readBytesAsUnsignedInt(bb, globalHeap.hdfBackingStorage.getSizeOfOffsets());
 			if (index == 0) {
 				//the size in global heap object 0 is the free space without counting object 0
-				size = size - 2 - 2 - 4 - globalHeap.hdfFc.getSizeOfOffsets();
+				size = size - 2 - 2 - 4 - globalHeap.hdfBackingStorage.getSizeOfOffsets();
 			}
 			data = createSubBuffer(bb, size);
 			seekBufferToNextMultipleOfEight(bb);

jhdf/src/main/java/io/jhdf/GroupImpl.java

@@ -42,11 +42,11 @@
 
 public class GroupImpl extends AbstractNode implements Group {
 	private final class ChildrenLazyInitializer extends LazyInitializer<Map<String, Node>> {
-		private final HdfBackingStorage hdfFc;
+		private final HdfBackingStorage hdfBackingStorage;
 		private final Group parent;
 
-		private ChildrenLazyInitializer(HdfBackingStorage hdfFc, Group parent) {
-			this.hdfFc = hdfFc;
+		private ChildrenLazyInitializer(HdfBackingStorage hdfBackingStorage, Group parent) {
+			this.hdfBackingStorage = hdfBackingStorage;
 			this.parent = parent;
 		}
 
@@ -74,17 +74,17 @@ private Map<String, Node> createNewStyleGroup(final ObjectHeader oh) {
 				logger.debug("Loaded group links from object header");
 			} else {
 				// Links are not stored compactly i.e in the fractal heap
-				final BTreeV2<LinkNameForIndexedGroupRecord> bTreeNode = new BTreeV2<>(hdfFc,
+				final BTreeV2<LinkNameForIndexedGroupRecord> bTreeNode = new BTreeV2<>(hdfBackingStorage,
 						linkInfoMessage.getBTreeNameIndexAddress());
-				final FractalHeap fractalHeap = new FractalHeap(hdfFc, linkInfoMessage.getFractalHeapAddress());
+				final FractalHeap fractalHeap = new FractalHeap(hdfBackingStorage, linkInfoMessage.getFractalHeapAddress());
 
 				List<LinkNameForIndexedGroupRecord> records = bTreeNode.getRecords();
 				links = new ArrayList<>(records.size());
 				for (LinkNameForIndexedGroupRecord linkName : records) {
 					ByteBuffer id = linkName.getId();
 					// Get the name data from the fractal heap
 					ByteBuffer bb = fractalHeap.getId(id);
-					links.add(LinkMessage.fromBuffer(bb, hdfFc.getSuperblock()));
+					links.add(LinkMessage.fromBuffer(bb, hdfBackingStorage.getSuperblock()));
 				}
 				logger.debug("Loaded group links from fractal heap");
 			}
@@ -114,15 +114,15 @@ private Map<String, Node> createNewStyleGroup(final ObjectHeader oh) {
 		private Map<String, Node> createOldStyleGroup(final ObjectHeader oh) {
 			logger.debug("Loading 'old' style group");
 			final SymbolTableMessage stm = oh.getMessageOfType(SymbolTableMessage.class);
-			final BTreeV1 rootBTreeNode = BTreeV1.createGroupBTree(hdfFc, stm.getBTreeAddress());
-			final LocalHeap rootNameHeap = new LocalHeap(hdfFc, stm.getLocalHeapAddress());
+			final BTreeV1 rootBTreeNode = BTreeV1.createGroupBTree(hdfBackingStorage, stm.getBTreeAddress());
+			final LocalHeap rootNameHeap = new LocalHeap(hdfBackingStorage, stm.getLocalHeapAddress());
 			final ByteBuffer nameBuffer = rootNameHeap.getDataBuffer();
 
 			final List<Long> childAddresses = rootBTreeNode.getChildAddresses();
 			final Map<String, Node> lazyChildren = new LinkedHashMap<>(childAddresses.size());
 
 			for (long child : childAddresses) {
-				GroupSymbolTableNode groupSTE = new GroupSymbolTableNode(hdfFc, child);
+				GroupSymbolTableNode groupSTE = new GroupSymbolTableNode(hdfBackingStorage, child);
 				for (SymbolTableEntry ste : groupSTE.getSymbolTableEntries()) {
 					String childName = readName(nameBuffer, ste.getLinkNameOffset());
 					final Node node;
@@ -132,7 +132,7 @@ private Map<String, Node> createOldStyleGroup(final ObjectHeader oh) {
 						break;
 					case 1: // Cached group
 						logger.trace("Creating group '{}'", childName);
-						node = createGroup(hdfFc, ste.getObjectHeaderAddress(), childName, parent);
+						node = createGroup(hdfBackingStorage, ste.getObjectHeaderAddress(), childName, parent);
 						break;
 					case 2: // Soft Link
 						logger.trace("Creating soft link '{}'", childName);
@@ -150,20 +150,20 @@ private Map<String, Node> createOldStyleGroup(final ObjectHeader oh) {
 		}
 
 		private Node createNode(String name, long address) {
-			final ObjectHeader linkHeader = ObjectHeader.readObjectHeader(hdfFc, address);
+			final ObjectHeader linkHeader = ObjectHeader.readObjectHeader(hdfBackingStorage, address);
 			final Node node;
 			if (linkHeader.hasMessageOfType(DataSpaceMessage.class)) {
 				// Its a a Dataset
 				logger.trace("Creating dataset [{}]", name);
-				node = DatasetLoader.createDataset(hdfFc, linkHeader, name, parent);
+				node = DatasetLoader.createDataset(hdfBackingStorage, linkHeader, name, parent);
 			} else if (linkHeader.hasMessageOfType(DataTypeMessage.class)) {
 				// Has a datatype but no dataspace so its a committed datatype
 				logger.trace("Creating committed data type [{}]", name);
-				node = new CommittedDatatype(hdfFc, address, name, parent);
+				node = new CommittedDatatype(hdfBackingStorage, address, name, parent);
 			} else {
 				// Its a group
 				logger.trace("Creating group [{}]", name);
-				node = createGroup(hdfFc, address, name, parent);
+				node = createGroup(hdfBackingStorage, address, name, parent);
 			}
 			return node;
 		}
@@ -178,29 +178,29 @@ private String readName(ByteBuffer bb, int linkNameOffset) {
 
 	private final LazyInitializer<Map<String, Node>> children;
 
-	private GroupImpl(HdfBackingStorage hdfFc, long address, String name, Group parent) {
-		super(hdfFc, address, name, parent);
+	private GroupImpl(HdfBackingStorage hdfBackingStorage, long address, String name, Group parent) {
+		super(hdfBackingStorage, address, name, parent);
 		logger.trace("Creating group '{}'...", name);
 
-		children = new ChildrenLazyInitializer(hdfFc, this);
+		children = new ChildrenLazyInitializer(hdfBackingStorage, this);
 
 		logger.debug("Created group '{}'", getPath());
 	}
 
 	/**
 	 * This is a special case constructor for the root group.
 	 *
-	 * @param hdfFc               The file channel for reading the file
+	 * @param hdfBackingStorage               The file channel for reading the file
 	 * @param objectHeaderAddress The offset into the file of the object header for
 	 *                            this group
 	 * @param parent              For the root group the parent is the file itself.
 	 */
-	private GroupImpl(HdfBackingStorage hdfFc, long objectHeaderAddress, HdfFile parent) {
-		super(hdfFc, objectHeaderAddress, "", parent); // No name special case for root group no name
+	private GroupImpl(HdfBackingStorage hdfBackingStorage, long objectHeaderAddress, HdfFile parent) {
+		super(hdfBackingStorage, objectHeaderAddress, "", parent); // No name special case for root group no name
 		logger.trace("Creating root group...");
 
 		// Special case for root group pass parent instead of this
-		children = new ChildrenLazyInitializer(hdfFc, parent);
+		children = new ChildrenLazyInitializer(hdfBackingStorage, parent);
 
 		logger.debug("Created root group of file '{}'", parent.getName());
 	}
@@ -209,21 +209,21 @@ private GroupImpl(HdfBackingStorage hdfFc, long objectHeaderAddress, HdfFile par
 	 * Creates a group for the specified object header with the given name by
 	 * reading from the file channel.
 	 *
-	 * @param hdfFc               The file channel for reading the file
+	 * @param hdfBackingStorage               The file channel for reading the file
 	 * @param objectHeaderAddress The offset into the file of the object header for
 	 *                            this group
 	 * @param name                The name of this group
 	 * @param parent              For the root group the parent is the file itself.
 	 * @return The newly read group
 	 */
-	/* package */ static Group createGroup(HdfBackingStorage hdfFc, long objectHeaderAddress, String name,
+	/* package */ static Group createGroup(HdfBackingStorage hdfBackingStorage, long objectHeaderAddress, String name,
 										   Group parent) {
-		return new GroupImpl(hdfFc, objectHeaderAddress, name, parent);
+		return new GroupImpl(hdfBackingStorage, objectHeaderAddress, name, parent);
 	}
 
-	/* package */ static Group createRootGroup(HdfBackingStorage hdfFc, long objectHeaderAddress, HdfFile file) {
+	/* package */ static Group createRootGroup(HdfBackingStorage hdfBackingStorage, long objectHeaderAddress, HdfFile file) {
 		// Call the special root group constructor
-		return new GroupImpl(hdfFc, objectHeaderAddress, file);
+		return new GroupImpl(hdfBackingStorage, objectHeaderAddress, file);
 	}
 
 	@Override

jhdf/src/main/java/io/jhdf/GroupSymbolTableNode.java

@@ -32,11 +32,11 @@ public class GroupSymbolTableNode {
 	private final short numberOfEntries;
 	private final SymbolTableEntry[] symbolTableEntries;
 
-	public GroupSymbolTableNode(HdfBackingStorage hdfFc, long address) {
+	public GroupSymbolTableNode(HdfBackingStorage hdfBackingStorage, long address) {
 		this.address = address;
 		try {
 			int headerSize = 8;
-			ByteBuffer header = hdfFc.readBufferFromAddress(address, headerSize);
+			ByteBuffer header = hdfBackingStorage.readBufferFromAddress(address, headerSize);
 
 			byte[] formatSignatureBytes = new byte[4];
 			header.get(formatSignatureBytes, 0, formatSignatureBytes.length);
@@ -59,12 +59,12 @@ public GroupSymbolTableNode(HdfBackingStorage hdfFc, long address) {
 			numberOfEntries = ByteBuffer.wrap(twoBytes).order(LITTLE_ENDIAN).getShort();
 			logger.trace("numberOfSymbols = {}", numberOfEntries);
 
-			final long symbolTableEntryBytes = hdfFc.getSizeOfOffsets() * 2L + 8L + 16L;
+			final long symbolTableEntryBytes = hdfBackingStorage.getSizeOfOffsets() * 2L + 8L + 16L;
 
 			symbolTableEntries = new SymbolTableEntry[numberOfEntries];
 			for (int i = 0; i < numberOfEntries; i++) {
 				long offset = address + headerSize + i * symbolTableEntryBytes;
-				symbolTableEntries[i] = new SymbolTableEntry(hdfFc, offset);
+				symbolTableEntries[i] = new SymbolTableEntry(hdfBackingStorage, offset);
 			}
 		} catch (Exception e) {
 			// TODO improve message