Add stream locations

src/main/java/org/scijava/io/handle/AbstractSeekableStreamHandle.java

@@ -0,0 +1,105 @@
+/*
+ * #%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.handle;
+
+import java.io.IOException;
+
+import org.scijava.io.location.Location;
+
+public abstract class AbstractSeekableStreamHandle<L extends Location> extends
+	AbstractStreamHandle<L> implements SeekableStreamHandle<L>
+{
+
+	private long jumpCutoff = 10000;
+
+	@Override
+	public void seek(final long pos) throws IOException {
+
+		// how much and which direction we have to jump
+		final long delta = pos - offset();
+
+		if (delta == 0) {
+			return;
+			// nothing to do
+		}
+		else if (delta > 0) {
+			// offset position is "downstream"
+
+			// try to reconnect instead of linearly reading large chunks
+			if (recreatePossible() && delta > jumpCutoff) {
+				recreateStreamFromPos(pos);
+			}
+			else {
+				jump(delta);
+			}
+
+		}
+		else { // delta < 0
+			// need to recreate the stream
+			if (recreatePossible()) {
+				recreateStreamFromPos(pos);
+			}
+			else {
+				resetStream();
+				jump(pos);
+			}
+		}
+		setOffset(pos);
+	}
+
+	/**
+	 * Recreates the internal input stream available through {@link #in()}, so
+	 * that it starts from the specified position.
+	 * 
+	 * @param pos
+	 * @throws IOException
+	 */
+	protected abstract void recreateStreamFromPos(long pos) throws IOException;
+
+	/**
+	 * In some implementations of this class, the ability to recreate the stream
+	 * depends on external factors (e.g. server support). This influences a
+	 * 
+	 * @return if recreate is actually possible.
+	 * @throws IOException
+	 */
+	protected abstract boolean recreatePossible() throws IOException;
+
+	/**
+	 * Sets the maximum of bytes which are read from the stream when seeking
+	 * forward. Any larger number will result in a call to
+	 * {@link #recreateStreamFromPos(long)}.
+	 */
+	protected void setJumpCutoff(long jumpCutoff) {
+		this.jumpCutoff = jumpCutoff;
+	}
+}

src/main/java/org/scijava/io/handle/AbstractStreamHandle.java

@@ -0,0 +1,65 @@
+/*
+ * #%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.handle;
+
+import org.scijava.io.location.Location;
+
+/**
+ * Abstract base class for {@link StreamHandle} implementations.
+ *
+ * @author Curtis Rueden
+ * @author Melissa Linkert
+ */
+public abstract class AbstractStreamHandle<L extends Location> extends
+	AbstractDataHandle<L> implements StreamHandle<L>
+{
+
+	// -- Fields --
+
+	/** Current position within the stream(s). */
+	private long offset;
+
+	// -- StreamHandle methods --
+
+	@Override
+	public void setOffset(final long offset) {
+		this.offset = offset;
+	}
+
+	// -- DataHandle methods --
+
+	@Override
+	public long offset() {
+		return offset;
+	}
+
+}

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

@@ -350,10 +350,7 @@ default String findString(final boolean saveString, final int blockSize,
 		final StringBuilder out = new StringBuilder();
 		final long startPos = offset();
 		long bytesDropped = 0;
-		final long inputLen = length();
-		long maxLen = inputLen - startPos;
-		final boolean tooLong = saveString && maxLen > MAX_SEARCH_SIZE;
-		if (tooLong) maxLen = MAX_SEARCH_SIZE;
+		final long maxLen = saveString ? MAX_SEARCH_SIZE : Long.MAX_VALUE;
 		boolean match = false;
 		int maxTermLen = 0;
 		for (final String term : terminators) {
@@ -366,7 +363,10 @@ default String findString(final boolean saveString, final int blockSize,
 			new DataHandleInputStream<>(this), getEncoding());
 		final char[] buf = new char[blockSize];
 		long loc = 0;
-		while (loc < maxLen && offset() < length() - 1) {
+		int r = 0;
+
+		// NB: we need at least 2 bytes to read a char
+		while (loc < maxLen && ((r = in.read(buf, 0, blockSize)) > 1)) {
 			// if we're not saving the string, drop any old, unnecessary output
 			if (!saveString) {
 				final int outLen = out.length();
@@ -378,16 +378,12 @@ default String findString(final boolean saveString, final int blockSize,
 					bytesDropped += dropIndex;
 				}
 			}
-
-			// read block from stream
-			final int r = in.read(buf, 0, blockSize);
-			if (r <= 0) throw new IOException("Cannot read from stream: " + r);
-
 			// append block to output
 			out.append(buf, 0, r);
 
 			// check output, returning smallest possible string
-			int min = Integer.MAX_VALUE, tagLen = 0;
+			int min = Integer.MAX_VALUE;
+			int tagLen = 0;
 			for (final String t : terminators) {
 				final int len = t.length();
 				final int start = (int) (loc - bytesDropped - len);
@@ -415,7 +411,9 @@ default String findString(final boolean saveString, final int blockSize,
 		}
 
 		// no match
-		if (tooLong) throw new IOException("Maximum search length reached.");
+		if (loc > MAX_SEARCH_SIZE) {
+			throw new IOException("Maximum search length reached.");
+		}
 		return saveString ? out.toString() : null;
 	}
 

src/main/java/org/scijava/io/handle/ResettableStreamHandle.java

@@ -0,0 +1,72 @@
+/*
+ * #%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.handle;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.scijava.io.location.Location;
+
+/**
+ * A {@link DataHandle} backed by an {@link InputStream} and/or
+ * {@link OutputStream}. Supports resetting the handle to the start of the
+ * internal stream(s).
+ */
+public interface ResettableStreamHandle<L extends Location> extends
+	StreamHandle<L>
+{
+
+	@Override
+	default void seek(final long pos) throws IOException {
+		final long off = offset();
+		if (pos == off) return; // nothing to do
+		if (pos > off) {
+			// jump from the current offset
+			jump(pos - off);
+		}
+		else {
+			// jump from the beginning of the stream
+			resetStream();
+			jump(pos);
+		}
+		setOffset(pos);
+	}
+
+	/**
+	 * Resets the stream to its start.
+	 *
+	 * @throws IOException If something goes wrong with the reset
+	 */
+	@Override
+	void resetStream() throws IOException;
+}

src/main/java/org/scijava/io/handle/SeekableStreamHandle.java

@@ -0,0 +1,53 @@
+/*
+ * #%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.handle;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.scijava.io.location.Location;
+
+/**
+ * A {@link DataHandle} backed by an {@link InputStream} and/or
+ * {@link OutputStream}. Supports seeking to an arbitrary position within the
+ * stream.
+ *
+ * @author Gabriel Einsdorf
+ */
+public interface SeekableStreamHandle<L extends Location> extends
+	ResettableStreamHandle<L>
+{
+
+	@Override
+	void seek(long pos) throws IOException;
+}