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Merge pull request #340 from scijava/stream-locations
Add stream locations
2 parents 6c094f7 + 183c2e4 commit b25bd7c

10 files changed

+644
-19
lines changed

Diff for: ‎src/main/java/org/scijava/io/handle/AbstractSeekableStreamHandle.java

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

Diff for: ‎src/main/java/org/scijava/io/handle/AbstractStreamHandle.java

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

Diff for: ‎src/main/java/org/scijava/io/handle/DataHandle.java

+10-12
Original file line numberDiff line numberDiff line change
@@ -350,10 +350,7 @@ default String findString(final boolean saveString, final int blockSize,
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final StringBuilder out = new StringBuilder();
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final long startPos = offset();
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long bytesDropped = 0;
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final long inputLen = length();
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long maxLen = inputLen - startPos;
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final boolean tooLong = saveString && maxLen > MAX_SEARCH_SIZE;
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if (tooLong) maxLen = MAX_SEARCH_SIZE;
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final long maxLen = saveString ? MAX_SEARCH_SIZE : Long.MAX_VALUE;
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boolean match = false;
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int maxTermLen = 0;
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for (final String term : terminators) {
@@ -366,7 +363,10 @@ default String findString(final boolean saveString, final int blockSize,
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new DataHandleInputStream<>(this), getEncoding());
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final char[] buf = new char[blockSize];
368365
long loc = 0;
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while (loc < maxLen && offset() < length() - 1) {
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int r = 0;
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// NB: we need at least 2 bytes to read a char
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while (loc < maxLen && ((r = in.read(buf, 0, blockSize)) > 1)) {
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// if we're not saving the string, drop any old, unnecessary output
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if (!saveString) {
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final int outLen = out.length();
@@ -378,16 +378,12 @@ default String findString(final boolean saveString, final int blockSize,
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bytesDropped += dropIndex;
379379
}
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}
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// read block from stream
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final int r = in.read(buf, 0, blockSize);
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if (r <= 0) throw new IOException("Cannot read from stream: " + r);
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386381
// append block to output
387382
out.append(buf, 0, r);
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389384
// check output, returning smallest possible string
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int min = Integer.MAX_VALUE, tagLen = 0;
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int min = Integer.MAX_VALUE;
386+
int tagLen = 0;
391387
for (final String t : terminators) {
392388
final int len = t.length();
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final int start = (int) (loc - bytesDropped - len);
@@ -415,7 +411,9 @@ default String findString(final boolean saveString, final int blockSize,
415411
}
416412

417413
// no match
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if (tooLong) throw new IOException("Maximum search length reached.");
414+
if (loc > MAX_SEARCH_SIZE) {
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throw new IOException("Maximum search length reached.");
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}
419417
return saveString ? out.toString() : null;
420418
}
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Diff for: ‎src/main/java/org/scijava/io/handle/ResettableStreamHandle.java

+72
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@@ -0,0 +1,72 @@
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/*
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* #%L
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* SciJava Common shared library for SciJava software.
4+
* %%
5+
* Copyright (C) 2009 - 2017 Board of Regents of the University of
6+
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
7+
* Institute of Molecular Cell Biology and Genetics.
8+
* %%
9+
* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
11+
*
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* 1. Redistributions of source code must retain the above copyright notice,
13+
* this list of conditions and the following disclaimer.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* and/or other materials provided with the distribution.
17+
*
18+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
22+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
29+
* #L%
30+
*/
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package org.scijava.io.handle;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import org.scijava.io.location.Location;
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/**
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* A {@link DataHandle} backed by an {@link InputStream} and/or
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* {@link OutputStream}. Supports resetting the handle to the start of the
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* internal stream(s).
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*/
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public interface ResettableStreamHandle<L extends Location> extends
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StreamHandle<L>
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{
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@Override
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default void seek(final long pos) throws IOException {
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final long off = offset();
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if (pos == off) return; // nothing to do
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if (pos > off) {
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// jump from the current offset
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jump(pos - off);
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}
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else {
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// jump from the beginning of the stream
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resetStream();
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jump(pos);
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}
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setOffset(pos);
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}
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/**
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* Resets the stream to its start.
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*
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* @throws IOException If something goes wrong with the reset
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*/
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@Override
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void resetStream() throws IOException;
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}

Diff for: ‎src/main/java/org/scijava/io/handle/SeekableStreamHandle.java

+53
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,53 @@
1+
/*
2+
* #%L
3+
* SciJava Common shared library for SciJava software.
4+
* %%
5+
* Copyright (C) 2009 - 2017 Board of Regents of the University of
6+
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
7+
* Institute of Molecular Cell Biology and Genetics.
8+
* %%
9+
* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
11+
*
12+
* 1. Redistributions of source code must retain the above copyright notice,
13+
* this list of conditions and the following disclaimer.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* and/or other materials provided with the distribution.
17+
*
18+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
22+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
29+
* #L%
30+
*/
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package org.scijava.io.handle;
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34+
import java.io.IOException;
35+
import java.io.InputStream;
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import java.io.OutputStream;
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import org.scijava.io.location.Location;
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/**
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* A {@link DataHandle} backed by an {@link InputStream} and/or
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* {@link OutputStream}. Supports seeking to an arbitrary position within the
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* stream.
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*
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* @author Gabriel Einsdorf
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*/
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public interface SeekableStreamHandle<L extends Location> extends
48+
ResettableStreamHandle<L>
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{
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@Override
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void seek(long pos) throws IOException;
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}

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