DataHandle: remove methods and classes refrencing java.nio

The java.nio package is not available on all JVMs so it's use must be
optional.

Author: gab1one

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

@@ -8,13 +8,13 @@
  * %%
  * 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
@@ -38,16 +38,15 @@
 import java.io.EOFException;
 import java.io.IOException;
 import java.io.InputStreamReader;
-import java.io.UTFDataFormatException;
 import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
 
+import org.scijava.io.bytes.BytesOrder;
 import org.scijava.plugin.WrapperPlugin;
 
 /**
  * A <em>data handle</em> is a plugin which provides both streaming and random
  * access to bytes at a {@link Location} (e.g., files or arrays).
- * 
+ *
  * @author Curtis Rueden
  * @see DataHandleInputStream
  * @see DataHandleOutputStream
@@ -76,15 +75,15 @@ public interface DataHandle<L extends Location> extends WrapperPlugin<L>,
 
 	/**
 	 * Sets the new length of the handle.
-	 * 
+	 *
 	 * @param length New length.
 	 * @throws IOException If there is an error changing the handle's length.
 	 */
 	void setLength(long length) throws IOException;
 
 	/**
-	 * Gets the number of bytes which can be read from, or written to, the
-	 * data handle, bounded by the specified number of bytes.
+	 * Gets the number of bytes which can be read from, or written to, the data
+	 * handle, bounded by the specified number of bytes.
 	 * <p>
 	 * In the case of reading, attempting to read the returned number of bytes is
 	 * guaranteed not to throw {@link EOFException}. However, be aware that the
@@ -106,8 +105,8 @@ public interface DataHandle<L extends Location> extends WrapperPlugin<L>,
 	 * </p>
 	 *
 	 * @param count Desired number of bytes to read/write.
-	 * @return The actual number of bytes which could be read/written,
-	 *         which might be less than the requested value.
+	 * @return The actual number of bytes which could be read/written, which might
+	 *         be less than the requested value.
 	 * @throws IOException If something goes wrong with the check.
 	 */
 	default long available(final long count) throws IOException {
@@ -123,7 +122,7 @@ default long available(final long count) throws IOException {
 
 	/**
 	 * Ensures that the handle has sufficient bytes available to read.
-	 * 
+	 *
 	 * @param count Number of bytes to read.
 	 * @see #available(long)
 	 * @throws EOFException If there are insufficient bytes available.
@@ -138,7 +137,7 @@ default void ensureReadable(final long count) throws IOException {
 	/**
 	 * Ensures that the handle has the correct length to be written to, and
 	 * extends it as required.
-	 * 
+	 *
 	 * @param count Number of bytes to write.
 	 * @return {@code true} if the handle's length was sufficient, or
 	 *         {@code false} if the handle's length required an extension.
@@ -157,42 +156,42 @@ default boolean ensureWritable(final long count) throws IOException {
 	}
 
 	/** Returns the byte order of the stream. */
-	ByteOrder getOrder();
+	BytesOrder getOrder();
 
 	/**
 	 * Sets the byte order of the stream.
 	 *
 	 * @param order Order to set.
 	 */
-	void setOrder(ByteOrder order);
+	void setOrder(BytesOrder order);
 
 	/**
-	 * Returns true iff the stream's order is {@link ByteOrder#BIG_ENDIAN}.
+	 * Returns true iff the stream's order is {@link BytesOrder#BIG_ENDIAN}.
 	 *
 	 * @see #getOrder()
 	 */
 	default boolean isBigEndian() {
-		return getOrder() == ByteOrder.BIG_ENDIAN;
+		return getOrder() == BytesOrder.BIG_ENDIAN;
 	}
 
 	/**
-	 * Returns true iff the stream's order is {@link ByteOrder#LITTLE_ENDIAN}.
+	 * Returns true iff the stream's order is {@link BytesOrder#LITTLE_ENDIAN}.
 	 *
 	 * @see #getOrder()
 	 */
 	default boolean isLittleEndian() {
-		return getOrder() == ByteOrder.LITTLE_ENDIAN;
+		return getOrder() == BytesOrder.LITTLE_ENDIAN;
 	}
 
 	/**
 	 * Sets the endianness of the stream.
 	 *
-	 * @param little If true, sets the order to {@link ByteOrder#LITTLE_ENDIAN};
-	 *          otherwise, sets the order to {@link ByteOrder#BIG_ENDIAN}.
-	 * @see #setOrder(ByteOrder)
+	 * @param little If true, sets the order to {@link BytesOrder#LITTLE_ENDIAN};
+	 *          otherwise, sets the order to {@link BytesOrder#BIG_ENDIAN}.
+	 * @see #setOrder(BytesOrder)
 	 */
 	default void setLittleEndian(final boolean little) {
-		setOrder(little ? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN);
+		setOrder(little ? BytesOrder.LITTLE_ENDIAN : BytesOrder.BIG_ENDIAN);
 	}
 
 	/** Gets the native encoding of the stream. */
@@ -201,62 +200,6 @@ default void setLittleEndian(final boolean little) {
 	/** Sets the native encoding of the stream. */
 	void setEncoding(String encoding);
 
-	/**
-	 * Reads up to {@code buf.remaining()} bytes of data from the stream into a
-	 * {@link ByteBuffer}.
-	 */
-	default int read(final ByteBuffer buf) throws IOException {
-		return read(buf, buf.remaining());
-	}
-
-	/**
-	 * Reads up to {@code len} bytes of data from the stream into a
-	 * {@link ByteBuffer}.
-	 * 
-	 * @return the total number of bytes read into the buffer.
-	 */
-	default int read(final ByteBuffer buf, final int len) throws IOException {
-		final int n;
-		if (buf.hasArray()) {
-			// read directly into the array
-			n = read(buf.array(), buf.arrayOffset(), len);
-		}
-		else {
-			// read into a temporary array, then copy
-			final byte[] b = new byte[len];
-			n = read(b);
-			buf.put(b, 0, n);
-		}
-		return n;
-	}
-
-	/**
-	 * Writes {@code buf.remaining()} bytes of data from the given
-	 * {@link ByteBuffer} to the stream.
-	 */
-	default void write(final ByteBuffer buf) throws IOException {
-		write(buf, buf.remaining());
-	}
-
-	/**
-	 * Writes {@code len} bytes of data from the given {@link ByteBuffer} to the
-	 * stream.
-	 */
-	default void write(final ByteBuffer buf, final int len)
-		throws IOException
-	{
-		if (buf.hasArray()) {
-			// write directly from the buffer's array
-			write(buf.array(), buf.arrayOffset(), len);
-		}
-		else {
-			// copy into a temporary array, then write
-			final byte[] b = new byte[len];
-			buf.get(b);
-			write(b);
-		}
-	}
-
 	/** Reads a string of arbitrary length, terminated by a null char. */
 	default String readCString() throws IOException {
 		final String line = findString("\0");
@@ -273,7 +216,7 @@ default String readString(final int n) throws IOException {
 
 	/**
 	 * Reads a string ending with one of the characters in the given string.
-	 * 
+	 *
 	 * @see #findString(String...)
 	 */
 	default String readString(final String lastChars) throws IOException {
@@ -287,7 +230,7 @@ default String readString(final String lastChars) throws IOException {
 
 	/**
 	 * Reads a string ending with one of the given terminating substrings.
-	 * 
+	 *
 	 * @param terminators The strings for which to search.
 	 * @return The string from the initial position through the end of the
 	 *         terminating sequence, or through the end of the stream if no
@@ -449,12 +392,13 @@ default int read() throws IOException {
 	 *
 	 * @return the total number of bytes read into the buffer.
 	 */
-	default int read(byte[] b) throws IOException {
+	default int read(final byte[] b) throws IOException {
 		return read(b, 0, b.length);
 	}
 
 	/**
-	 * Reads up to len bytes of data from the stream into an array of bytes.
+	 * Reads up to {@code len} bytes of data from the stream into an array of
+	 * bytes.
 	 *
 	 * @return the total number of bytes read into the buffer.
 	 */

src/main/java/org/scijava/io/bytes/BytesOrder.java

@@ -0,0 +1,39 @@
+/*
+ * #%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.bytes;
+
+/**
+ * @author gabriel
+ */
+public enum BytesOrder {
+		LITTLE_ENDIAN, BIG_ENDIAN
+}

src/main/java/org/scijava/io/location/AbstractDataHandle.java

@@ -8,13 +8,13 @@
  * %%
  * 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
@@ -31,10 +31,9 @@
 
 package org.scijava.io.location;
 
-import java.nio.ByteOrder;
-
 import org.scijava.io.DataHandle;
 import org.scijava.io.Location;
+import org.scijava.io.bytes.BytesOrder;
 import org.scijava.plugin.AbstractWrapperPlugin;
 
 /**
@@ -48,18 +47,18 @@ public abstract class AbstractDataHandle<L extends Location> extends
 
 	// -- Fields --
 
-	private ByteOrder order = ByteOrder.BIG_ENDIAN;
+	private BytesOrder order = BytesOrder.BIG_ENDIAN;
 	private String encoding = "UTF-8";
 
 	// -- DataHandle methods --
 
 	@Override
-	public ByteOrder getOrder() {
+	public BytesOrder getOrder() {
 		return order;
 	}
 
 	@Override
-	public void setOrder(final ByteOrder order) {
+	public void setOrder(final BytesOrder order) {
 		this.order = order;
 	}
 

src/test/java/org/scijava/ContextCreationTest.java

@@ -8,13 +8,13 @@
  * %%
  * 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
@@ -55,7 +55,7 @@
 
 /**
  * Tests {@link Context} creation with {@link Service} dependencies.
- * 
+ *
  * @author Curtis Rueden
  */
 public class ContextCreationTest {
@@ -97,8 +97,8 @@ public void testFull() {
 				org.scijava.input.DefaultInputService.class,
 				org.scijava.io.DefaultDataHandleService.class,
 				org.scijava.io.DefaultIOService.class,
-				org.scijava.io.nio.DefaultNIOService.class,
 				org.scijava.io.DefaultRecentFileService.class,
+				org.scijava.io.nio.DefaultNIOService.class,
 				org.scijava.main.DefaultMainService.class,
 				org.scijava.menu.DefaultMenuService.class,
 				org.scijava.module.DefaultModuleService.class,