Merge pull request #259 from scijava/more-handles-gabriel

Finalize Location / DataHandle API  and add more Locations

Author: ctrueden

src/main/java/org/scijava/io/ByteArrayByteBank.java

@@ -0,0 +1,143 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import org.scijava.util.ByteArray;
+
+/**
+ * {@link ByteBank} implementation backed by a {@link ByteArray}. Self-growing
+ * up to a maximum capacity of {@link Integer#MAX_VALUE}
+ *
+ * @author Gabriel Einsdorf
+ */
+public class ByteArrayByteBank implements ByteBank {
+
+	private final ByteArray buffer;
+	private long maxBufferedPos = -1;
+
+	/**
+	 * Creates a {@link ByteArrayByteBank}
+	 */
+	public ByteArrayByteBank() {
+		buffer = new ByteArray();
+	}
+
+	/**
+	 * Creates a {@link ByteArrayByteBank} with the specified initial capacity
+	 *
+	 * @param initialCapacity the initial capacity of this {@link ByteBank}
+	 */
+	public ByteArrayByteBank(final int initialCapacity) {
+		buffer = new ByteArray(initialCapacity);
+	}
+
+	/**
+	 * Creates a {@link ByteArrayByteBank} that wraps the specified
+	 * {@link ByteArray}.
+	 *
+	 * @param bytes the {@link ByteArray} to wrap
+	 */
+	public ByteArrayByteBank(final ByteArray bytes) {
+		buffer = bytes;
+		bytes.size();
+	}
+
+	/**
+	 * Creates a {@link ByteArrayByteBank} that wraps the provided byte array
+	 *
+	 * @param bytes the bytes to wrap
+	 */
+	public ByteArrayByteBank(final byte[] bytes) {
+		buffer = new ByteArray(bytes);
+		maxBufferedPos = bytes.length;
+	}
+
+	@Override
+	public long getMaxBufferSize() {
+		return Integer.MAX_VALUE;
+	}
+
+	@Override
+	public void setBytes(final long startpos, final byte[] bytes,
+		final int offset, final int length)
+	{
+		// ensure we have space
+		checkWritePos(startpos, startpos + length);
+		final int neededCapacity = (int) (Math.max(maxBufferedPos, 0) + length);
+		buffer.ensureCapacity(neededCapacity);
+
+		// copy the data
+		System.arraycopy(bytes, offset, buffer.getArray(), (int) startpos, length);
+		buffer.setSize(neededCapacity);
+		updateMaxPos(startpos + length);
+	}
+
+	@Override
+	public void setByte(final long pos, final byte b) {
+		checkWritePos(pos, pos);
+		buffer.setValue((int) pos, b);
+		updateMaxPos(pos);
+	}
+
+	private void updateMaxPos(final long pos) {
+		maxBufferedPos = pos > maxBufferedPos ? pos : maxBufferedPos;
+	}
+
+	@Override
+	public void clear() {
+		buffer.clear();
+		maxBufferedPos = 0;
+	}
+
+	@Override
+	public byte getByte(final long pos) {
+		checkReadPos(pos, pos);
+		// the buffer might contain bytes with negative value
+		// we need to flip the sign to positive to satisfy the method contract
+		return buffer.getValue((int) pos);
+	}
+
+	@Override
+	public int getBytes(final long startPos, final byte[] b, final int offset,
+		final int length)
+	{
+		checkReadPos(startPos, startPos + length);
+		final int readLength = (int) Math.min(getMaxPos() - startPos, length);
+		System.arraycopy(buffer.getArray(), (int) startPos, b, offset, readLength);
+		return readLength;
+	}
+
+	@Override
+	public long getMaxPos() {
+		return maxBufferedPos;
+	}
+}

src/main/java/org/scijava/io/ByteBank.java

@@ -0,0 +1,169 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+/**
+ * A {@link ByteBank} is a self-growing buffer over arbitrary bytes.
+ *
+ * @author Gabriel Einsdorf
+ */
+public interface ByteBank {
+
+	/**
+	 * @param pos the position to read from
+	 * @return the byte at the given position
+	 */
+	public byte getByte(long pos);
+
+	/**
+	 * @param startPos the position in the buffer to start reading from
+	 * @param bytes the byte array to read into
+	 * @return the number of bytes read
+	 */
+	default int getBytes(long startPos, byte[] bytes) {
+		return getBytes(startPos, bytes, 0, bytes.length);
+	}
+
+	/**
+	 * @param startPos the position in the buffer to start reading from
+	 * @param bytes the byte array to read into
+	 * @param offset the offset in the bytes array
+	 * @param length the number of elements to read into the bytes array
+	 * @return number of bytes read
+	 */
+	int getBytes(long startPos, byte[] bytes, int offset, int length);
+
+	/**
+	 * Sets the bytes starting form the given position to the values form the
+	 * provided array.
+	 *
+	 * @param startPos the position in the buffer to start writing from
+	 * @param bytes the byte array to write
+	 * @param offset the offset in the bytes array
+	 * @param length the number of bytes to read
+	 */
+	void setBytes(long startPos, byte[] bytes, int offset, int length);
+
+	/**
+	 * Appends the given bytes to the buffer
+	 *
+	 * @param bytes the array containing the bytes to append to the buffer
+	 * @param length the number of elements to append from the bytes array
+	 */
+	default void appendBytes(byte[] bytes, int length) {
+		setBytes(getMaxPos() + 1, bytes, 0, length);
+	}
+
+	/**
+	 * Check if we can read from the specified range
+	 *
+	 * @param start the start position of the range
+	 * @param end the end position of the range
+	 */
+	default void checkReadPos(final long start, final long end) {
+		basicRangeCheck(start, end);
+		if (start > getMaxPos()) {
+			throw new IndexOutOfBoundsException("Requested position: " + start +
+				" is larger than the maximally buffered postion: " + getMaxPos());
+		}
+	}
+
+	/**
+	 * Check if we can write to the specified range
+	 *
+	 * @param start the start position of the range
+	 * @param end the end position of the range
+	 * @throws IndexOutOfBoundsException if
+	 */
+	default void checkWritePos(final long start, final long end) {
+		if (start > getMaxPos() + 1) { // we can't have holes in the buffer
+			throw new IndexOutOfBoundsException("Requested start position: " + start +
+				" would leave a hole in the buffer, largest legal position is: " +
+				getMaxPos() + 1);
+		}
+		if (end < start) {
+			throw new IllegalArgumentException(
+				"Invalid range, end is smaller than start!");
+		}
+		if (end > getMaxBufferSize()) {
+			throw new IndexOutOfBoundsException("Requested postion " + end +
+				" is larger than the maximal buffer size: " + getMaxPos());
+		}
+	}
+
+	/**
+	 * Ensures that the requested range satisfies basic sanity criteria.
+	 *
+	 * @param start the start of the range
+	 * @param end the end of the range
+	 */
+	default void basicRangeCheck(final long start, final long end) {
+		if (start > getMaxPos()) {
+			throw new IndexOutOfBoundsException("Requested postion " + start +
+				" is larger than the maximal buffer size: " + getMaxPos());
+		}
+		if (end < start) {
+			throw new IllegalArgumentException(
+				"Invalid range, end is smaller than start!");
+		}
+	}
+
+	/**
+	 * Clears the buffer
+	 */
+	void clear();
+
+	/**
+	 * @return the position of the last byte in this ByteBank
+	 */
+	long getMaxPos();
+
+	/**
+	 * Sets the byte at the given position
+	 *
+	 * @param pos the position
+	 * @param b the value to set
+	 */
+	void setByte(long pos, byte b);
+
+	/**
+	 * @return the maximal size of the buffer
+	 */
+	long getMaxBufferSize();
+
+	/**
+	 * @return True iff the buffer is read-only.
+	 */
+	default boolean isReadOnly() {
+		return false;
+	}
+}