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Add IOBuffer interface + ByteArray implementation
Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
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‎src/main/java/org/scijava/io/ByteArrayIOBuffer.java‎

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/*
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* #%L
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* SciJava Common shared library for SciJava software.
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* %%
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* Copyright (C) 2009 - 2017 Board of Regents of the University of
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* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
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* Institute of Molecular Cell Biology and Genetics.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.io;
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import org.scijava.util.ByteArray;
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/**
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* {@link IOBuffer} implementation backed by a {@link ByteArray}.
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*
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* @author Gabriel Einsdorf
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*/
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public class ByteArrayIOBuffer implements IOBuffer {
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private ByteArray buffer;
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private long maxBufferedPos = -1;
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public ByteArrayIOBuffer() {
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buffer = new ByteArray();
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}
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@Override
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public int getMaxBufferSize() {
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return Integer.MAX_VALUE;
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}
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@Override
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public void setBytes(long startpos, byte[] bytes, int offset, int length) {
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// ensure we have space
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checkWritePos(startpos, startpos + length);
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int neededCapacity = (int) (Math.max(maxBufferedPos, 0) + length);
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buffer.ensureCapacity(neededCapacity);
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// copy the data
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System.arraycopy(bytes, offset, buffer.getArray(), (int) startpos, length);
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buffer.setSize(neededCapacity);
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updateMaxPos(startpos + length);
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}
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@Override
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public void setByte(long pos, byte b) {
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checkWritePos(pos, pos);
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buffer.setValue((int) pos, b);
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updateMaxPos(pos);
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}
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private void updateMaxPos(long pos) {
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maxBufferedPos = pos > maxBufferedPos ? pos : maxBufferedPos;
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}
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@Override
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public void clear() {
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buffer.clear();
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maxBufferedPos = 0;
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}
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@Override
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public byte getByte(long pos) {
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checkReadPos(pos, pos);
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// the buffer might contain bytes with negative value
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// we need to flip the sign to positive to satisfy the method contract
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return buffer.getValue((int) pos);
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}
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@Override
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public int getBytes(long startPos, byte[] b, int offset, int length) {
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checkReadPos(startPos, startPos + length);
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System.arraycopy(buffer.getArray(), (int) startPos, b, offset, length);
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return length;
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}
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@Override
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public long getMaxPos() {
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return maxBufferedPos;
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}
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/**
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* Ensures that the requested range satisfies basic sanity criteria.
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*
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* @param start the start of the range
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* @param end the end of the range
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*/
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private void basicRangeCheck(long start, long end) {
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if (start > Integer.MAX_VALUE) {
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throw new IndexOutOfBoundsException("Requested postion " + start +
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" is larger than the maximal buffer size: " + Integer.MAX_VALUE);
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}
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if (end > Integer.MAX_VALUE) {
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throw new IndexOutOfBoundsException("Requested postion " + end +
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" is larger than the maximal buffer size: " + Integer.MAX_VALUE);
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}
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if (end < start) {
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throw new IllegalArgumentException(
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"Invalid range, end is smaller than start!");
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}
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}
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/**
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* Check if we can write to the specified range
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*
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* @param start the start position of the range
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* @param end the end position of the range
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*/
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private void checkWritePos(long start, long end) {
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basicRangeCheck(start, end);
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if (start > maxBufferedPos + 1) { // we can't have holes in the buffer
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throw new IndexOutOfBoundsException("Requested start position: " + start +
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" would leave a hole in the buffer, largest legal position is: " +
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maxBufferedPos + 1);
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}
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}
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/**
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* Check if we can read from the specified range
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*
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* @param start the start position of the range
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* @param end the end position of the range
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*/
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private void checkReadPos(long start, long end) {
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basicRangeCheck(start, end);
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if (start > maxBufferedPos) {
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throw new IndexOutOfBoundsException("Reuested position: " + start +
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" is larger than the maximally buffered postion: " + maxBufferedPos);
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}
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if (end > maxBufferedPos) {
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throw new IndexOutOfBoundsException("reuested position: " + end +
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" is larger than the maximally buffered postion: " + maxBufferedPos);
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}
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}
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}

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

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/*
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* #%L
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* SciJava Common shared library for SciJava software.
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* %%
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* Copyright (C) 2009 - 2017 Board of Regents of the University of
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* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
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* Institute of Molecular Cell Biology and Genetics.
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* %%
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* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.io;
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/**
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* Self-growing buffer over arbitrary bytes.
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*
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* @author Gabriel Einsdorf
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*/
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public interface IOBuffer {
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/**
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* @param pos the position to read from
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* @return the byte at the given position
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*/
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public byte getByte(long pos);
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/**
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* @param startPos the position in the buffer to start reading from
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* @param bytes the byte array to read into
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* @return the number of bytes read
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*/
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default int getBytes(long startPos, byte[] bytes) {
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return getBytes(startPos, bytes, 0, bytes.length);
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}
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/**
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* @param startPos the position in the buffer to start reading from
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* @param bytes the byte array to read into
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* @param offset the offset in the bytes array
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* @param length the number of elements to read into the bytes array
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* @return number of bytes read
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*/
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int getBytes(long startPos, byte[] bytes, int offset, int length);
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/**
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* Sets the bytes starting form the given position to the values form the
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* provided array.
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*
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* @param startPos the position in the buffer to start writing from
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* @param bytes the byte array to write
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* @param offset the offset in the bytes array
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* @param length the number of bytes to read
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*/
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void setBytes(long startPos, byte[] bytes, int offset, int length);
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/**
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* Appends the given bytes to the buffer
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*
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* @param bytes the bytes to append to the buffer
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* @param length the number of elements to append from the bytes array
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*/
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default void appendBytes(byte[] bytes, int length) {
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setBytes(getMaxPos() + 1, bytes, 0, length);
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}
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/**
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* Clears the buffer
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*/
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public void clear();
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/**
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* @return the largest bufferd position
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*/
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public long getMaxPos();
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/**
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* Sets the byte at the given position
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*
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* @param pos the position
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* @param b the value to set
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*/
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void setByte(long pos, byte b);
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/**
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* @return the max size of the buffer
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*/
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public int getMaxBufferSize();
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}

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