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SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by both ImageJ and SCIFIO.
/*
* #%L
* SciJava Common shared library for SciJava software.
* %%
* Copyright (C) 2009 - 2016 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
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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package org.scijava.io;
import java.io.Closeable;
import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import org.scijava.plugin.WrapperPlugin;
/**
* A data handle is a plugin which provides access to bytes in a data
* stream (e.g., files or arrays), identified by a {@link Location}.
*
* @author Curtis Rueden
* @see DataHandleInputStream
* @see DataHandleOutputStream
*/
public interface DataHandle extends WrapperPlugin,
DataInput, DataOutput, Closeable
{
/** Default block size to use when searching through the stream. */
int DEFAULT_BLOCK_SIZE = 256 * 1024; // 256 KB
/** Default bound on bytes to search when searching through the stream. */
int MAX_SEARCH_SIZE = 512 * 1024 * 1024; // 512 MB
/** Returns the current offset in the stream. */
long offset() throws IOException;
/** Returns the length of the stream. */
long length() throws IOException;
/**
* Returns the current order of the stream.
*
* @return See above.
*/
ByteOrder getOrder();
/** Gets the endianness of the stream. */
default boolean isLittleEndian() {
return getOrder() == ByteOrder.LITTLE_ENDIAN;
}
/**
* Sets the byte order of the stream.
*
* @param order Order to set.
*/
void setOrder(ByteOrder order);
/** Sets the endianness of the stream. */
default void setOrder(final boolean little) {
setOrder(little ? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN);
}
/** Gets the native encoding of the stream. */
String getEncoding();
/** 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;
}
/**
* Sets the stream pointer offset, measured from the beginning of the stream,
* at which the next read or write occurs.
*/
void seek(long pos) throws IOException;
/**
* Writes up to {@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 up to len bytes of data from the given 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");
return line.length() == 0 ? null : line;
}
/** Reads a string of up to length n. */
default String readString(int n) throws IOException {
final long avail = length() - offset();
if (n > avail) n = (int) avail;
final byte[] b = new byte[n];
readFully(b);
return new String(b, getEncoding());
}
/**
* Reads a string ending with one of the characters in the given string.
*
* @see #findString(String...)
*/
default String readString(final String lastChars) throws IOException {
if (lastChars.length() == 1) return findString(lastChars);
final String[] terminators = new String[lastChars.length()];
for (int i = 0; i < terminators.length; i++) {
terminators[i] = lastChars.substring(i, i + 1);
}
return findString(terminators);
}
/**
* 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
* terminating sequence is found.
*/
default String findString(final String... terminators) throws IOException {
return findString(true, DEFAULT_BLOCK_SIZE, terminators);
}
/**
* Reads or skips a string ending with one of the given terminating
* substrings.
*
* @param saveString Whether to collect the string from the current file
* pointer to the terminating bytes, and return it. If false, returns
* null.
* @param terminators The strings for which to search.
* @throws IOException If saveString flag is set and the maximum search length
* (512 MB) is exceeded.
* @return The string from the initial position through the end of the
* terminating sequence, or through the end of the stream if no
* terminating sequence is found, or null if saveString flag is unset.
*/
default String findString(final boolean saveString,
final String... terminators) throws IOException
{
return findString(saveString, DEFAULT_BLOCK_SIZE, terminators);
}
/**
* Reads a string ending with one of the given terminating substrings, using
* the specified block size for buffering.
*
* @param blockSize The block size to use when reading bytes in chunks.
* @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
* terminating sequence is found.
*/
default String findString(final int blockSize, final String... terminators)
throws IOException
{
return findString(true, blockSize, terminators);
}
/**
* Reads or skips a string ending with one of the given terminating
* substrings, using the specified block size for buffering.
*
* @param saveString Whether to collect the string from the current file
* pointer to the terminating bytes, and return it. If false, returns
* null.
* @param blockSize The block size to use when reading bytes in chunks.
* @param terminators The strings for which to search.
* @throws IOException If saveString flag is set and the maximum search length
* (512 MB) is exceeded.
* @return The string from the initial position through the end of the
* terminating sequence, or through the end of the stream if no
* terminating sequence is found, or null if saveString flag is unset.
*/
default String findString(final boolean saveString, final int blockSize,
final String... terminators) throws IOException
{
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;
boolean match = false;
int maxTermLen = 0;
for (final String term : terminators) {
final int len = term.length();
if (len > maxTermLen) maxTermLen = len;
}
@SuppressWarnings("resource")
final InputStreamReader in =
new InputStreamReader(new DataHandleInputStream<>(this), getEncoding());
final char[] buf = new char[blockSize];
long loc = 0;
while (loc < maxLen && offset() < length() - 1) {
// if we're not saving the string, drop any old, unnecessary output
if (!saveString) {
final int outLen = out.length();
if (outLen >= maxTermLen) {
final int dropIndex = outLen - maxTermLen + 1;
final String last = out.substring(dropIndex, outLen);
out.setLength(0);
out.append(last);
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;
for (final String t : terminators) {
final int len = t.length();
final int start = (int) (loc - bytesDropped - len);
final int value = out.indexOf(t, start < 0 ? 0 : start);
if (value >= 0 && value < min) {
match = true;
min = value;
tagLen = len;
}
}
if (match) {
// reset stream to proper location
seek(startPos + bytesDropped + min + tagLen);
// trim output string
if (saveString) {
out.setLength(min + tagLen);
return out.toString();
}
return null;
}
loc += r;
}
// no match
if (tooLong) throw new IOException("Maximum search length reached.");
return saveString ? out.toString() : null;
}
// -- InputStream look-alikes --
/**
* Reads the next byte of data from the stream.
*
* @return the next byte of data, or -1 if the end of the stream is reached.
* @throws IOException - if an I/O error occurs.
*/
int read() throws IOException;
/**
* Reads up to b.length bytes of data from the stream into an array of bytes.
*
* @return the total number of bytes read into the buffer.
*/
default int read(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.
*
* @return the total number of bytes read into the buffer.
*/
int read(byte[] b, int off, int len) throws IOException;
/**
* Skips over and discards {@code n} bytes of data from the stream. The
* {@code skip} method may, for a variety of reasons, end up skipping over
* some smaller number of bytes, possibly {@code 0}. This may result from any
* of a number of conditions; reaching end of file before {@code n} bytes have
* been skipped is only one possibility. The actual number of bytes skipped is
* returned. If {@code n} is negative, no bytes are skipped.
*
* @param n - the number of bytes to be skipped.
* @return the actual number of bytes skipped.
* @throws IOException - if an I/O error occurs.
*/
default long skip(final long n) throws IOException {
if (n < 0) return 0;
final long remain = length() - offset();
final long num = n < remain ? n : remain;
seek(offset() + num);
return num;
}
}