/*
    * Copyright (C) 2009, Google Inc.
    * Copyright (C) 2008-2009, Johannes E. Schindelin <johannes.schindelin@gmx.de>
    * and other copyright owners as documented in the project's IP log.
    *
    * This program and the accompanying materials are made available
    * under the terms of the Eclipse Distribution License v1.0 which
    * accompanies this distribution, is reproduced below, and is
    * available at http://www.eclipse.org/org/documents/edl-v10.php
   *
   * All rights reserved.
   *
   * Redistribution and use in source and binary forms, with or
   * without modification, are permitted provided that the following
   * conditions are met:
   *
   * - Redistributions of source code must retain the above copyright
   *   notice, this list of conditions and the following disclaimer.
   *
   * - 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.
   *
   * - Neither the name of the Eclipse Foundation, Inc. nor the
   *   names of its contributors may be used to endorse or promote
   *   products derived from this software without specific prior
   *   written permission.
   *
   * 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 OWNER 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.
   */
  
  package org.eclipse.jgit.diff;
  
  import static org.eclipse.jgit.diff.DiffEntry.ChangeType.ADD;
  import static org.eclipse.jgit.diff.DiffEntry.ChangeType.COPY;
  import static org.eclipse.jgit.diff.DiffEntry.ChangeType.DELETE;
  import static org.eclipse.jgit.diff.DiffEntry.ChangeType.MODIFY;
  import static org.eclipse.jgit.diff.DiffEntry.ChangeType.RENAME;
  import static org.eclipse.jgit.diff.DiffEntry.Side.NEW;
  import static org.eclipse.jgit.diff.DiffEntry.Side.OLD;
  import static org.eclipse.jgit.lib.Constants.encode;
  import static org.eclipse.jgit.lib.Constants.encodeASCII;
  import static org.eclipse.jgit.lib.FileMode.GITLINK;
  
  import java.io.ByteArrayOutputStream;
  import java.io.IOException;
  import java.io.OutputStream;
  import java.util.Collection;
  import java.util.Collections;
  import java.util.List;
  
  import org.eclipse.jgit.diff.DiffAlgorithm.SupportedAlgorithm;
  import org.eclipse.jgit.diff.DiffEntry.ChangeType;
  import org.eclipse.jgit.dircache.DirCacheIterator;
  import org.eclipse.jgit.errors.AmbiguousObjectException;
  import org.eclipse.jgit.errors.BinaryBlobException;
  import org.eclipse.jgit.errors.CancelledException;
  import org.eclipse.jgit.errors.CorruptObjectException;
  import org.eclipse.jgit.errors.IncorrectObjectTypeException;
  import org.eclipse.jgit.errors.MissingObjectException;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.lib.AbbreviatedObjectId;
  import org.eclipse.jgit.lib.AnyObjectId;
  import org.eclipse.jgit.lib.Config;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectLoader;
  import org.eclipse.jgit.lib.ObjectReader;
  import org.eclipse.jgit.lib.ProgressMonitor;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.patch.FileHeader;
  import org.eclipse.jgit.patch.FileHeader.PatchType;
  import org.eclipse.jgit.revwalk.FollowFilter;
  import org.eclipse.jgit.revwalk.RevTree;
  import org.eclipse.jgit.revwalk.RevWalk;
  import org.eclipse.jgit.storage.pack.PackConfig;
  import org.eclipse.jgit.treewalk.AbstractTreeIterator;
  import org.eclipse.jgit.treewalk.CanonicalTreeParser;
  import org.eclipse.jgit.treewalk.EmptyTreeIterator;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.treewalk.WorkingTreeIterator;
  import org.eclipse.jgit.treewalk.filter.AndTreeFilter;
  import org.eclipse.jgit.treewalk.filter.IndexDiffFilter;
  import org.eclipse.jgit.treewalk.filter.NotIgnoredFilter;
 import org.eclipse.jgit.treewalk.filter.PathFilter;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.eclipse.jgit.util.LfsFactory;
 import org.eclipse.jgit.util.QuotedString;
 
 /**
  * Format a Git style patch script.
  */
 public class DiffFormatter implements AutoCloseable {
 	private static final int DEFAULT_BINARY_FILE_THRESHOLD = PackConfig.DEFAULT_BIG_FILE_THRESHOLD;
 
 	private static final byte[] noNewLine = encodeASCII("\\ No newline at end of file\n"); //$NON-NLS-1$
 
 	/** Magic return content indicating it is empty or no content present. */
 	private static final byte[] EMPTY = new byte[] {};
 
 	private final OutputStream out;
 
 	private ObjectReader reader;
 
 	private boolean closeReader;
 
 	private DiffConfig diffCfg;
 
 	private int context = 3;
 
 	private int abbreviationLength = 7;
 
 	private DiffAlgorithm diffAlgorithm;
 
 	private RawTextComparator comparator = RawTextComparator.DEFAULT;
 
 	private int binaryFileThreshold = DEFAULT_BINARY_FILE_THRESHOLD;
 
 	private String oldPrefix = "a/"; //$NON-NLS-1$
 
 	private String newPrefix = "b/"; //$NON-NLS-1$
 
 	private TreeFilter pathFilter = TreeFilter.ALL;
 
 	private RenameDetector renameDetector;
 
 	private ProgressMonitor progressMonitor;
 
 	private ContentSource.Pair source;
 
 	private Repository repository;
 
 	/**
 	 * Create a new formatter with a default level of context.
 	 *
 	 * @param out
 	 *            the stream the formatter will write line data to. This stream
 	 *            should have buffering arranged by the caller, as many small
 	 *            writes are performed to it.
 	 */
 	public DiffFormatter(OutputStream out) {
 		this.out = out;
 	}
 
 	/**
 	 * Get output stream
 	 *
 	 * @return the stream we are outputting data to
 	 */
 	protected OutputStream getOutputStream() {
 		return out;
 	}
 
 	/**
 	 * Set the repository the formatter can load object contents from.
 	 *
 	 * Once a repository has been set, the formatter must be released to ensure
 	 * the internal ObjectReader is able to release its resources.
 	 *
 	 * @param repository
 	 *            source repository holding referenced objects.
 	 */
 	public void setRepository(Repository repository) {
 		this.repository = repository;
 		setReader(repository.newObjectReader(), repository.getConfig(), true);
 	}
 
 	/**
 	 * Set the repository the formatter can load object contents from.
 	 *
 	 * @param reader
 	 *            source reader holding referenced objects. Caller is responsible
 	 *            for closing the reader.
 	 * @param cfg
 	 *            config specifying diff algorithm and rename detection options.
 	 * @since 4.5
 	 */
 	public void setReader(ObjectReader reader, Config cfg) {
 		setReader(reader, cfg, false);
 	}
 
 	private void setReader(ObjectReader reader, Config cfg, boolean closeReader) {
 		close();
 		this.closeReader = closeReader;
 		this.reader = reader;
 		this.diffCfg = cfg.get(DiffConfig.KEY);
 
 		ContentSource cs = ContentSource.create(reader);
 		source = new ContentSource.Pair(cs, cs);
 
 		if (diffCfg.isNoPrefix()) {
 			setOldPrefix(""); //$NON-NLS-1$
 			setNewPrefix(""); //$NON-NLS-1$
 		}
 		setDetectRenames(diffCfg.isRenameDetectionEnabled());
 
 		diffAlgorithm = DiffAlgorithm.getAlgorithm(cfg.getEnum(
 				ConfigConstants.CONFIG_DIFF_SECTION, null,
 				ConfigConstants.CONFIG_KEY_ALGORITHM,
 				SupportedAlgorithm.HISTOGRAM));
 	}
 
 	/**
 	 * Change the number of lines of context to display.
 	 *
 	 * @param lineCount
 	 *            number of lines of context to see before the first
 	 *            modification and after the last modification within a hunk of
 	 *            the modified file.
 	 */
 	public void setContext(int lineCount) {
 		if (lineCount < 0)
 			throw new IllegalArgumentException(
 					JGitText.get().contextMustBeNonNegative);
 		context = lineCount;
 	}
 
 	/**
 	 * Change the number of digits to show in an ObjectId.
 	 *
 	 * @param count
 	 *            number of digits to show in an ObjectId.
 	 */
 	public void setAbbreviationLength(int count) {
 		if (count < 0)
 			throw new IllegalArgumentException(
 					JGitText.get().abbreviationLengthMustBeNonNegative);
 		abbreviationLength = count;
 	}
 
 	/**
 	 * Set the algorithm that constructs difference output.
 	 *
 	 * @param alg
 	 *            the algorithm to produce text file differences.
 	 * @see HistogramDiff
 	 */
 	public void setDiffAlgorithm(DiffAlgorithm alg) {
 		diffAlgorithm = alg;
 	}
 
 	/**
 	 * Set the line equivalence function for text file differences.
 	 *
 	 * @param cmp
 	 *            The equivalence function used to determine if two lines of
 	 *            text are identical. The function can be changed to ignore
 	 *            various types of whitespace.
 	 * @see RawTextComparator#DEFAULT
 	 * @see RawTextComparator#WS_IGNORE_ALL
 	 * @see RawTextComparator#WS_IGNORE_CHANGE
 	 * @see RawTextComparator#WS_IGNORE_LEADING
 	 * @see RawTextComparator#WS_IGNORE_TRAILING
 	 */
 	public void setDiffComparator(RawTextComparator cmp) {
 		comparator = cmp;
 	}
 
 	/**
 	 * Set maximum file size for text files.
 	 *
 	 * Files larger than this size will be treated as though they are binary and
 	 * not text. Default is {@value #DEFAULT_BINARY_FILE_THRESHOLD} .
 	 *
 	 * @param threshold
 	 *            the limit, in bytes. Files larger than this size will be
 	 *            assumed to be binary, even if they aren't.
 	 */
 	public void setBinaryFileThreshold(int threshold) {
 		this.binaryFileThreshold = threshold;
 	}
 
 	/**
 	 * Set the prefix applied in front of old file paths.
 	 *
 	 * @param prefix
 	 *            the prefix in front of old paths. Typically this is the
 	 *            standard string {@code "a/"}, but may be any prefix desired by
 	 *            the caller. Must not be null. Use the empty string to have no
 	 *            prefix at all.
 	 */
 	public void setOldPrefix(String prefix) {
 		oldPrefix = prefix;
 	}
 
 	/**
 	 * Get the prefix applied in front of old file paths.
 	 *
 	 * @return the prefix
 	 * @since 2.0
 	 */
 	public String getOldPrefix() {
 		return this.oldPrefix;
 	}
 
 	/**
 	 * Set the prefix applied in front of new file paths.
 	 *
 	 * @param prefix
 	 *            the prefix in front of new paths. Typically this is the
 	 *            standard string {@code "b/"}, but may be any prefix desired by
 	 *            the caller. Must not be null. Use the empty string to have no
 	 *            prefix at all.
 	 */
 	public void setNewPrefix(String prefix) {
 		newPrefix = prefix;
 	}
 
 	/**
 	 * Get the prefix applied in front of new file paths.
 	 *
 	 * @return the prefix
 	 * @since 2.0
 	 */
 	public String getNewPrefix() {
 		return this.newPrefix;
 	}
 
 	/**
 	 * Get if rename detection is enabled
 	 *
 	 * @return true if rename detection is enabled
 	 */
 	public boolean isDetectRenames() {
 		return renameDetector != null;
 	}
 
 	/**
 	 * Enable or disable rename detection.
 	 *
 	 * Before enabling rename detection the repository must be set with
 	 * {@link #setRepository(Repository)}. Once enabled the detector can be
 	 * configured away from its defaults by obtaining the instance directly from
 	 * {@link #getRenameDetector()} and invoking configuration.
 	 *
 	 * @param on
 	 *            if rename detection should be enabled.
 	 */
 	public void setDetectRenames(boolean on) {
 		if (on && renameDetector == null) {
 			assertHaveReader();
 			renameDetector = new RenameDetector(reader, diffCfg);
 		} else if (!on)
 			renameDetector = null;
 	}
 
 	/**
 	 * Get rename detector
 	 *
 	 * @return the rename detector if rename detection is enabled
 	 */
 	public RenameDetector getRenameDetector() {
 		return renameDetector;
 	}
 
 	/**
 	 * Set the progress monitor for long running rename detection.
 	 *
 	 * @param pm
 	 *            progress monitor to receive rename detection status through.
 	 */
 	public void setProgressMonitor(ProgressMonitor pm) {
 		progressMonitor = pm;
 	}
 
 	/**
 	 * Set the filter to produce only specific paths.
 	 *
 	 * If the filter is an instance of
 	 * {@link org.eclipse.jgit.revwalk.FollowFilter}, the filter path will be
 	 * updated during successive scan or format invocations. The updated path
 	 * can be obtained from {@link #getPathFilter()}.
 	 *
 	 * @param filter
 	 *            the tree filter to apply.
 	 */
 	public void setPathFilter(TreeFilter filter) {
 		pathFilter = filter != null ? filter : TreeFilter.ALL;
 	}
 
 	/**
 	 * Get path filter
 	 *
 	 * @return the current path filter
 	 */
 	public TreeFilter getPathFilter() {
 		return pathFilter;
 	}
 
 	/**
 	 * Flush the underlying output stream of this formatter.
 	 *
 	 * @throws java.io.IOException
 	 *             the stream's own flush method threw an exception.
 	 */
 	public void flush() throws IOException {
 		out.flush();
 	}
 
 	/**
 	 * {@inheritDoc}
 	 * <p>
 	 * Release the internal ObjectReader state.
 	 *
 	 * @since 4.0
 	 */
 	@Override
 	public void close() {
 		if (reader != null && closeReader) {
 			reader.close();
 		}
 	}
 
 	/**
 	 * Determine the differences between two trees.
 	 *
 	 * No output is created, instead only the file paths that are different are
 	 * returned. Callers may choose to format these paths themselves, or convert
 	 * them into {@link org.eclipse.jgit.patch.FileHeader} instances with a
 	 * complete edit list by calling {@link #toFileHeader(DiffEntry)}.
 	 * <p>
 	 * Either side may be null to indicate that the tree has beed added or
 	 * removed. The diff will be computed against nothing.
 	 *
 	 * @param a
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
 	 * @return the paths that are different.
 	 * @throws java.io.IOException
 	 *             trees cannot be read or file contents cannot be read.
 	 */
 	public List<DiffEntry> scan(AnyObjectId="../../../../org/eclipse/jgit/lib/AnyObjectId.html#AnyObjectId">AnyObjectId a, AnyObjectId b)
 			throws IOException {
 		assertHaveReader();
 
 		try (RevWalkRevWalk.html#RevWalk">RevWalk rw = new RevWalk(reader)) {
 			RevTree aTree = a != null ? rw.parseTree(a) : null;
 			RevTree bTree = b != null ? rw.parseTree(b) : null;
 			return scan(aTree, bTree);
 		}
 	}
 
 	/**
 	 * Determine the differences between two trees.
 	 *
 	 * No output is created, instead only the file paths that are different are
 	 * returned. Callers may choose to format these paths themselves, or convert
 	 * them into {@link org.eclipse.jgit.patch.FileHeader} instances with a
 	 * complete edit list by calling {@link #toFileHeader(DiffEntry)}.
 	 * <p>
 	 * Either side may be null to indicate that the tree has beed added or
 	 * removed. The diff will be computed against nothing.
 	 *
 	 * @param a
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
 	 * @return the paths that are different.
 	 * @throws java.io.IOException
 	 *             trees cannot be read or file contents cannot be read.
 	 */
 	public List<DiffEntry> scan(RevTreehref="../../../../org/eclipse/jgit/revwalk/RevTree.html#RevTree">RevTree a, RevTree b) throws IOException {
 		assertHaveReader();
 
 		AbstractTreeIterator aIterator = makeIteratorFromTreeOrNull(a);
 		AbstractTreeIterator bIterator = makeIteratorFromTreeOrNull(b);
 		return scan(aIterator, bIterator);
 	}
 
 	private AbstractTreeIterator makeIteratorFromTreeOrNull(RevTree tree)
 			throws IncorrectObjectTypeException, IOException {
 		if (tree != null) {
 			CanonicalTreeParser parser = new CanonicalTreeParser();
 			parser.reset(reader, tree);
 			return parser;
 		} else
 			return new EmptyTreeIterator();
 	}
 
 	/**
 	 * Determine the differences between two trees.
 	 *
 	 * No output is created, instead only the file paths that are different are
 	 * returned. Callers may choose to format these paths themselves, or convert
 	 * them into {@link org.eclipse.jgit.patch.FileHeader} instances with a
 	 * complete edit list by calling {@link #toFileHeader(DiffEntry)}.
 	 *
 	 * @param a
 	 *            the old (or previous) side.
 	 * @param b
 	 *            the new (or updated) side.
 	 * @return the paths that are different.
 	 * @throws java.io.IOException
 	 *             trees cannot be read or file contents cannot be read.
 	 */
 	public List<DiffEntry> scan(AbstractTreeIterator./../org/eclipse/jgit/treewalk/AbstractTreeIterator.html#AbstractTreeIterator">AbstractTreeIterator a, AbstractTreeIterator b)
 			throws IOException {
 		assertHaveReader();
 
 		TreeWalk walk = new TreeWalk(reader);
 		walk.addTree(a);
 		walk.addTree(b);
 		walk.setRecursive(true);
 
 		TreeFilter filter = getDiffTreeFilterFor(a, b);
 		if (pathFilter instanceof FollowFilter) {
 			walk.setFilter(AndTreeFilter.create(
 					PathFilter.create(((FollowFilter) pathFilter).getPath()),
 					filter));
 		} else {
 			walk.setFilter(AndTreeFilter.create(pathFilter, filter));
 		}
 
 		source = new ContentSource.Pair(source(a), source(b));
 
 		List<DiffEntry> files = DiffEntry.scan(walk);
 		if (pathFilter instanceof FollowFilter && isAdd(files)) {
 			// The file we are following was added here, find where it
 			// came from so we can properly show the rename or copy,
 			// then continue digging backwards.
 			//
 			a.reset();
 			b.reset();
 			walk.reset();
 			walk.addTree(a);
 			walk.addTree(b);
 			walk.setFilter(filter);
 
 			if (renameDetector == null)
 				setDetectRenames(true);
 			files = updateFollowFilter(detectRenames(DiffEntry.scan(walk)));
 
 		} else if (renameDetector != null)
 			files = detectRenames(files);
 
 		return files;
 	}
 
 	private static TreeFilter getDiffTreeFilterFor(AbstractTreeIterator a,
 			AbstractTreeIterator b) {
 		if (a instanceof DirCacheIterator && b instanceof WorkingTreeIterator)
 			return new IndexDiffFilter(0, 1);
 
 		if (a instanceof WorkingTreeIterator && b instanceof DirCacheIterator)
 			return new IndexDiffFilter(1, 0);
 
 		TreeFilter filter = TreeFilter.ANY_DIFF;
 		if (a instanceof WorkingTreeIterator)
 			filter = AndTreeFilter.create(new NotIgnoredFilter(0), filter);
 		if (b instanceof WorkingTreeIterator)
 			filter = AndTreeFilter.create(new NotIgnoredFilter(1), filter);
 		return filter;
 	}
 
 	private ContentSource source(AbstractTreeIterator iterator) {
 		if (iterator instanceof WorkingTreeIterator)
 			return ContentSource.create((WorkingTreeIterator) iterator);
 		return ContentSource.create(reader);
 	}
 
 	private List<DiffEntry> detectRenames(List<DiffEntry> files)
 			throws IOException {
 		renameDetector.reset();
 		renameDetector.addAll(files);
 		try {
 			return renameDetector.compute(reader, progressMonitor);
 		} catch (CancelledException e) {
 			// TODO: consider propagating once bug 536323 is tackled
 			// (making DiffEntry.scan() and DiffFormatter.scan() and
 			// format() cancellable).
 			return Collections.emptyList();
 		}
 	}
 
 	private boolean isAdd(List<DiffEntry> files) {
 		String oldPath = ((FollowFilter) pathFilter).getPath();
 		for (DiffEntry ent : files) {
 			if (ent.getChangeType() == ADD && ent.getNewPath().equals(oldPath))
 				return true;
 		}
 		return false;
 	}
 
 	private List<DiffEntry> updateFollowFilter(List<DiffEntry> files) {
 		String oldPath = ((FollowFilter) pathFilter).getPath();
 		for (DiffEntry ent : files) {
 			if (isRename(ent) && ent.getNewPath().equals(oldPath)) {
 				pathFilter = FollowFilter.create(ent.getOldPath(), diffCfg);
 				return Collections.singletonList(ent);
 			}
 		}
 		return Collections.emptyList();
 	}
 
 	private static boolean isRename(DiffEntry ent) {
 		return ent.getChangeType() == RENAME || ent.getChangeType() == COPY;
 	}
 
 	/**
 	 * Format the differences between two trees.
 	 *
 	 * The patch is expressed as instructions to modify {@code a} to make it
 	 * {@code b}.
 	 * <p>
 	 * Either side may be null to indicate that the tree has beed added or
 	 * removed. The diff will be computed against nothing.
 	 *
 	 * @param a
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
 	 * @throws java.io.IOException
 	 *             trees cannot be read, file contents cannot be read, or the
 	 *             patch cannot be output.
 	 */
 	public void format(AnyObjectId="../../../../org/eclipse/jgit/lib/AnyObjectId.html#AnyObjectId">AnyObjectId a, AnyObjectId b) throws IOException {
 		format(scan(a, b));
 	}
 
 	/**
 	 * Format the differences between two trees.
 	 *
 	 * The patch is expressed as instructions to modify {@code a} to make it
 	 * {@code b}.
 	 *
 	 * <p>
 	 * Either side may be null to indicate that the tree has beed added or
 	 * removed. The diff will be computed against nothing.
 	 *
 	 * @param a
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
 	 * @throws java.io.IOException
 	 *             trees cannot be read, file contents cannot be read, or the
 	 *             patch cannot be output.
 	 */
 	public void format(RevTreehref="../../../../org/eclipse/jgit/revwalk/RevTree.html#RevTree">RevTree a, RevTree b) throws IOException {
 		format(scan(a, b));
 	}
 
 	/**
 	 * Format the differences between two trees.
 	 *
 	 * The patch is expressed as instructions to modify {@code a} to make it
 	 * {@code b}.
 	 * <p>
 	 * Either side may be null to indicate that the tree has beed added or
 	 * removed. The diff will be computed against nothing.
 	 *
 	 * @param a
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
 	 * @throws java.io.IOException
 	 *             trees cannot be read, file contents cannot be read, or the
 	 *             patch cannot be output.
 	 */
 	public void format(AbstractTreeIterator./../org/eclipse/jgit/treewalk/AbstractTreeIterator.html#AbstractTreeIterator">AbstractTreeIterator a, AbstractTreeIterator b)
 			throws IOException {
 		format(scan(a, b));
 	}
 
 	/**
 	 * Format a patch script from a list of difference entries. Requires
 	 * {@link #scan(AbstractTreeIterator, AbstractTreeIterator)} to have been
 	 * called first.
 	 *
 	 * @param entries
 	 *            entries describing the affected files.
 	 * @throws java.io.IOException
 	 *             a file's content cannot be read, or the output stream cannot
 	 *             be written to.
 	 */
 	public void format(List<? extends DiffEntry> entries) throws IOException {
 		for (DiffEntry ent : entries)
 			format(ent);
 	}
 
 	/**
 	 * Format a patch script for one file entry.
 	 *
 	 * @param ent
 	 *            the entry to be formatted.
 	 * @throws java.io.IOException
 	 *             a file's content cannot be read, or the output stream cannot
 	 *             be written to.
 	 */
 	public void format(DiffEntry ent) throws IOException {
 		FormatResult res = createFormatResult(ent);
 		format(res.header, res.a, res.b);
 	}
 
 	private static byte[] writeGitLinkText(AbbreviatedObjectId id) {
 		if (ObjectId.zeroId().equals(id.toObjectId())) {
 			return EMPTY;
 		}
 		return encodeASCII("Subproject commit " + id.name() //$NON-NLS-1$
 				+ "\n"); //$NON-NLS-1$
 	}
 
 	private String format(AbbreviatedObjectId id) {
 		if (id.isComplete() && reader != null) {
 			try {
 				id = reader.abbreviate(id.toObjectId(), abbreviationLength);
 			} catch (IOException cannotAbbreviate) {
 				// Ignore this. We'll report the full identity.
 			}
 		}
 		return id.name();
 	}
 
 	private static String quotePath(String name) {
 		return QuotedString.GIT_PATH.quote(name);
 	}
 
 	/**
 	 * Format a patch script, reusing a previously parsed FileHeader.
 	 * <p>
 	 * This formatter is primarily useful for editing an existing patch script
 	 * to increase or reduce the number of lines of context within the script.
 	 * All header lines are reused as-is from the supplied FileHeader.
 	 *
 	 * @param head
 	 *            existing file header containing the header lines to copy.
 	 * @param a
 	 *            text source for the pre-image version of the content. This
 	 *            must match the content of
 	 *            {@link org.eclipse.jgit.patch.FileHeader#getOldId()}.
 	 * @param b
 	 *            text source for the post-image version of the content. This
 	 *            must match the content of
 	 *            {@link org.eclipse.jgit.patch.FileHeader#getNewId()}.
 	 * @throws java.io.IOException
 	 *             writing to the supplied stream failed.
 	 */
 	public void format(FileHeader head, RawTexthref="../../../../org/eclipse/jgit/diff/RawText.html#RawText">RawText a, RawText b)
 			throws IOException {
 		// Reuse the existing FileHeader as-is by blindly copying its
 		// header lines, but avoiding its hunks. Instead we recreate
 		// the hunks from the text instances we have been supplied.
 		//
 		final int start = head.getStartOffset();
 		int end = head.getEndOffset();
 		if (!head.getHunks().isEmpty())
 			end = head.getHunks().get(0).getStartOffset();
 		out.write(head.getBuffer(), start, end - start);
 		if (head.getPatchType() == PatchType.UNIFIED)
 			format(head.toEditList(), a, b);
 	}
 
 	/**
 	 * Formats a list of edits in unified diff format
 	 *
 	 * @param edits
 	 *            some differences which have been calculated between A and B
 	 * @param a
 	 *            the text A which was compared
 	 * @param b
 	 *            the text B which was compared
 	 * @throws java.io.IOException
 	 */
 	public void format(EditList edits, RawTexthref="../../../../org/eclipse/jgit/diff/RawText.html#RawText">RawText a, RawText b)
 			throws IOException {
 		for (int curIdx = 0; curIdx < edits.size();) {
 			Edit curEdit = edits.get(curIdx);
 			final int endIdx = findCombinedEnd(edits, curIdx);
 			final Edit endEdit = edits.get(endIdx);
 
 			int aCur = (int) Math.max(0, (long) curEdit.getBeginA() - context);
 			int bCur = (int) Math.max(0, (long) curEdit.getBeginB() - context);
 			final int aEnd = (int) Math.min(a.size(), (long) endEdit.getEndA() + context);
 			final int bEnd = (int) Math.min(b.size(), (long) endEdit.getEndB() + context);
 
 			writeHunkHeader(aCur, aEnd, bCur, bEnd);
 
 			while (aCur < aEnd || bCur < bEnd) {
 				if (aCur < curEdit.getBeginA() || endIdx + 1 < curIdx) {
 					writeContextLine(a, aCur);
 					if (isEndOfLineMissing(a, aCur))
 						out.write(noNewLine);
 					aCur++;
 					bCur++;
 				} else if (aCur < curEdit.getEndA()) {
 					writeRemovedLine(a, aCur);
 					if (isEndOfLineMissing(a, aCur))
 						out.write(noNewLine);
 					aCur++;
 				} else if (bCur < curEdit.getEndB()) {
 					writeAddedLine(b, bCur);
 					if (isEndOfLineMissing(b, bCur))
 						out.write(noNewLine);
 					bCur++;
 				}
 
 				if (end(curEdit, aCur, bCur) && ++curIdx < edits.size())
 					curEdit = edits.get(curIdx);
 			}
 		}
 	}
 
 	/**
 	 * Output a line of context (unmodified line).
 	 *
 	 * @param text
 	 *            RawText for accessing raw data
 	 * @param line
 	 *            the line number within text
 	 * @throws java.io.IOException
 	 */
 	protected void writeContextLine(RawText text, int line)
 			throws IOException {
 		writeLine(' ', text, line);
 	}
 
 	private static boolean isEndOfLineMissing(RawText text, int line) {
 		return line + 1 == text.size() && text.isMissingNewlineAtEnd();
 	}
 
 	/**
 	 * Output an added line.
 	 *
 	 * @param text
 	 *            RawText for accessing raw data
 	 * @param line
 	 *            the line number within text
 	 * @throws java.io.IOException
 	 */
 	protected void writeAddedLine(RawText text, int line)
 			throws IOException {
 		writeLine('+', text, line);
 	}
 
 	/**
 	 * Output a removed line
 	 *
 	 * @param text
 	 *            RawText for accessing raw data
 	 * @param line
 	 *            the line number within text
 	 * @throws java.io.IOException
 	 */
 	protected void writeRemovedLine(RawText text, int line)
 			throws IOException {
 		writeLine('-', text, line);
 	}
 
 	/**
 	 * Output a hunk header
 	 *
 	 * @param aStartLine
 	 *            within first source
 	 * @param aEndLine
 	 *            within first source
 	 * @param bStartLine
 	 *            within second source
 	 * @param bEndLine
 	 *            within second source
 	 * @throws java.io.IOException
 	 */
 	protected void writeHunkHeader(int aStartLine, int aEndLine,
 			int bStartLine, int bEndLine) throws IOException {
 		out.write('@');
 		out.write('@');
 		writeRange('-', aStartLine + 1, aEndLine - aStartLine);
 		writeRange('+', bStartLine + 1, bEndLine - bStartLine);
 		out.write(' ');
 		out.write('@');
 		out.write('@');
 		out.write('\n');
 	}
 
 	private void writeRange(char prefix, int begin, int cnt)
 			throws IOException {
 		out.write(' ');
 		out.write(prefix);
 		switch (cnt) {
 		case 0:
 			// If the range is empty, its beginning number must be the
 			// line just before the range, or 0 if the range is at the
 			// start of the file stream. Here, begin is always 1 based,
 			// so an empty file would produce "0,0".
 			//
 			out.write(encodeASCII(begin - 1));
 			out.write(',');
 			out.write('0');
 			break;
 
 		case 1:
 			// If the range is exactly one line, produce only the number.
 			//
 			out.write(encodeASCII(begin));
 			break;
 
 		default:
 			out.write(encodeASCII(begin));
 			out.write(',');
 			out.write(encodeASCII(cnt));
 			break;
 		}
 	}
 
 	/**
 	 * Write a standard patch script line.
 	 *
 	 * @param prefix
 	 *            prefix before the line, typically '-', '+', ' '.
 	 * @param text
 	 *            the text object to obtain the line from.
 	 * @param cur
 	 *            line number to output.
 	 * @throws java.io.IOException
 	 *             the stream threw an exception while writing to it.
 	 */
 	protected void writeLine(final char prefix, final RawText text,
 			final int cur) throws IOException {
 		out.write(prefix);
 		text.writeLine(out, cur);
 		out.write('\n');
 	}
 
 	/**
 	 * Creates a {@link org.eclipse.jgit.patch.FileHeader} representing the
 	 * given {@link org.eclipse.jgit.diff.DiffEntry}
 	 * <p>
 	 * This method does not use the OutputStream associated with this
 	 * DiffFormatter instance. It is therefore safe to instantiate this
 	 * DiffFormatter instance with a
 	 * {@link org.eclipse.jgit.util.io.DisabledOutputStream} if this method is
 	 * the only one that will be used.
 	 *
 	 * @param ent
 	 *            the DiffEntry to create the FileHeader for
 	 * @return a FileHeader representing the DiffEntry. The FileHeader's buffer
 	 *         will contain only the header of the diff output. It will also
 	 *         contain one {@link org.eclipse.jgit.patch.HunkHeader}.
 	 * @throws java.io.IOException
 	 *             the stream threw an exception while writing to it, or one of
 	 *             the blobs referenced by the DiffEntry could not be read.
 	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             one of the blobs referenced by the DiffEntry is corrupt.
 	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             one of the blobs referenced by the DiffEntry is missing.
 	 */
 	public FileHeader toFileHeader(DiffEntry ent) throws IOException,
 			CorruptObjectException, MissingObjectException {
 		return createFormatResult(ent).header;
 	}
 
 	private static class FormatResult {
 		FileHeader header;
 
 		RawText a;
 
 		RawText b;
 	}
 
 	private FormatResult createFormatResult(DiffEntry ent) throws IOException,
 			CorruptObjectException, MissingObjectException {
 		final FormatResult res = new FormatResult();
 		ByteArrayOutputStream buf = new ByteArrayOutputStream();
 		final EditList editList;
 		final FileHeader.PatchType type;
 
 		formatHeader(buf, ent);
 
 		if (ent.getOldId() == null || ent.getNewId() == null) {
 			// Content not changed (e.g. only mode, pure rename)
 			editList = new EditList();
 			type = PatchType.UNIFIED;
 			res.header = new FileHeader(buf.toByteArray(), editList, type);
 			return res;
 		}
 
 		assertHaveReader();
 
 		RawText aRaw = null;
 		RawText bRaw = null;
 		if (ent.getOldMode() == GITLINK || ent.getNewMode() == GITLINK) {
 			aRaw = new RawText(writeGitLinkText(ent.getOldId()));
 			bRaw = new RawText(writeGitLinkText(ent.getNewId()));
 		} else {
 			try {
 				aRaw = open(OLD, ent);
 				bRaw = open(NEW, ent);
 			} catch (BinaryBlobException e) {
 				// Do nothing; we check for null below.
 				formatOldNewPaths(buf, ent);
 				buf.write(encodeASCII("Binary files differ\n")); //$NON-NLS-1$
 				editList = new EditList();
 				type = PatchType.BINARY;
 				res.header = new FileHeader(buf.toByteArray(), editList, type);
 				return res;
 			}
 		}
 
 		res.a = aRaw;
 		res.b = bRaw;
 		editList = diff(res.a, res.b);
 		type = PatchType.UNIFIED;
 
 		switch (ent.getChangeType()) {
 			case RENAME:
 			case COPY:
 				if (!editList.isEmpty())
 					formatOldNewPaths(buf, ent);
 				break;
 
 			default:
 				formatOldNewPaths(buf, ent);
 				break;
 		}
 
 
 		res.header = new FileHeader(buf.toByteArray(), editList, type);
 		return res;
 	}
 
 	private EditList diff(RawTexthref="../../../../org/eclipse/jgit/diff/RawText.html#RawText">RawText a, RawText b) {
 		return diffAlgorithm.diff(comparator, a, b);
 	}
 
 	private void assertHaveReader() {
 		if (reader == null) {
 			throw new IllegalStateException(JGitText.get().readerIsRequired);
 		}
 	}
 
 	private RawText open(DiffEntry.Side side, DiffEntry entry)
 			throws IOException, BinaryBlobException {
 		if (entry.getMode(side) == FileMode.MISSING)
 			return RawText.EMPTY_TEXT;
 
 		if (entry.getMode(side).getObjectType() != Constants.OBJ_BLOB)
 			return RawText.EMPTY_TEXT;
 
 		AbbreviatedObjectId id = entry.getId(side);
 		if (!id.isComplete()) {
 			Collection<ObjectId> ids = reader.resolve(id);
 			if (ids.size() == 1) {
 				id = AbbreviatedObjectId.fromObjectId(ids.iterator().next());
 				switch (side) {
 				case OLD:
 					entry.oldId = id;
 					break;
 				case NEW:
 					entry.newId = id;
 					break;
 				}
 			} else if (ids.isEmpty())
 				throw new MissingObjectException(id, Constants.OBJ_BLOB);
 			else
 				throw new AmbiguousObjectException(id, ids);
 		}
 
 		ObjectLoader ldr = LfsFactory.getInstance().applySmudgeFilter(repository,
 				source.open(side, entry), entry.getDiffAttribute());
 		return RawText.load(ldr, binaryFileThreshold);
 	}
 
 	/**
 	 * Output the first header line
 	 *
 	 * @param o
 	 *            The stream the formatter will write the first header line to
 	 * @param type
 	 *            The {@link org.eclipse.jgit.diff.DiffEntry.ChangeType}
 	 * @param oldPath
 	 *            old path to the file
 	 * @param newPath
 	 *            new path to the file
 	 * @throws java.io.IOException
 	 *             the stream threw an exception while writing to it.
 	 */
 	protected void formatGitDiffFirstHeaderLine(ByteArrayOutputStream o,
 			final ChangeType type, final String oldPath, final String newPath)
 			throws IOException {
 		o.write(encodeASCII("diff --git ")); //$NON-NLS-1$
 		o.write(encode(quotePath(oldPrefix + (type == ADD ? newPath : oldPath))));
 		o.write(' ');
 		o.write(encode(quotePath(newPrefix
 				+ (type == DELETE ? oldPath : newPath))));
 		o.write('\n');
 	}
 
 	private void formatHeader(ByteArrayOutputStream o, DiffEntry ent)
 			throws IOException {
 		final ChangeType type = ent.getChangeType();
 		final String oldp = ent.getOldPath();
 		final String newp = ent.getNewPath();
 		final FileMode oldMode = ent.getOldMode();
 		final FileMode newMode = ent.getNewMode();
 
 		formatGitDiffFirstHeaderLine(o, type, oldp, newp);
 
 		if ((type == MODIFY || type == COPY || type == RENAME)
 				&& !oldMode.equals(newMode)) {
 			o.write(encodeASCII("old mode ")); //$NON-NLS-1$
 			oldMode.copyTo(o);
 			o.write('\n');
 
 			o.write(encodeASCII("new mode ")); //$NON-NLS-1$
 			newMode.copyTo(o);
 			o.write('\n');
 		}
 
 		switch (type) {
 		case ADD:
 			o.write(encodeASCII("new file mode ")); //$NON-NLS-1$
 			newMode.copyTo(o);
 			o.write('\n');
 			break;
 
 		case DELETE:
 			o.write(encodeASCII("deleted file mode ")); //$NON-NLS-1$
 			oldMode.copyTo(o);
 			o.write('\n');
 			break;
 
 		case RENAME:
 			o.write(encodeASCII("similarity index " + ent.getScore() + "%")); //$NON-NLS-1$ //$NON-NLS-2$
 			o.write('\n');
 
 			o.write(encode("rename from " + quotePath(oldp))); //$NON-NLS-1$
 			o.write('\n');
 
 			o.write(encode("rename to " + quotePath(newp))); //$NON-NLS-1$
 			o.write('\n');
 			break;
 
 		case COPY:
 			o.write(encodeASCII("similarity index " + ent.getScore() + "%")); //$NON-NLS-1$ //$NON-NLS-2$
 			o.write('\n');
 
 			o.write(encode("copy from " + quotePath(oldp))); //$NON-NLS-1$
 			o.write('\n');
 
 			o.write(encode("copy to " + quotePath(newp))); //$NON-NLS-1$
 			o.write('\n');
 			break;
 
 		case MODIFY:
 			if (0 < ent.getScore()) {
 				o.write(encodeASCII("dissimilarity index " //$NON-NLS-1$
 						+ (100 - ent.getScore()) + "%")); //$NON-NLS-1$
 				o.write('\n');
 			}
 			break;
 		}
 
 		if (ent.getOldId() != null && !ent.getOldId().equals(ent.getNewId())) {
 			formatIndexLine(o, ent);
 		}
 	}
 
 	/**
 	 * Format index line
 	 *
 	 * @param o
 	 *            the stream the formatter will write line data to
 	 * @param ent
 	 *            the DiffEntry to create the FileHeader for
 	 * @throws java.io.IOException
 	 *             writing to the supplied stream failed.
 	 */
 	protected void formatIndexLine(OutputStream o, DiffEntry ent)
 			throws IOException {
 		o.write(encodeASCII("index " // //$NON-NLS-1$
 				+ format(ent.getOldId()) //
 				+ ".." // //$NON-NLS-1$
 				+ format(ent.getNewId())));
 		if (ent.getOldMode().equals(ent.getNewMode())) {
 			o.write(' ');
 			ent.getNewMode().copyTo(o);
 		}
 		o.write('\n');
 	}
 
 	private void formatOldNewPaths(ByteArrayOutputStream o, DiffEntry ent)
 			throws IOException {
 		if (ent.oldId.equals(ent.newId))
 			return;
 
 		final String oldp;
 		final String newp;
 
 		switch (ent.getChangeType()) {
 		case ADD:
 			oldp = DiffEntry.DEV_NULL;
 			newp = quotePath(newPrefix + ent.getNewPath());
 			break;
 
 		case DELETE:
 			oldp = quotePath(oldPrefix + ent.getOldPath());
 			newp = DiffEntry.DEV_NULL;
 			break;
 
 		default:
 			oldp = quotePath(oldPrefix + ent.getOldPath());
 			newp = quotePath(newPrefix + ent.getNewPath());
 			break;
 		}
 
 		o.write(encode("--- " + oldp + "\n")); //$NON-NLS-1$ //$NON-NLS-2$
 		o.write(encode("+++ " + newp + "\n")); //$NON-NLS-1$ //$NON-NLS-2$
 	}
 
 	private int findCombinedEnd(List<Edit> edits, int i) {
 		int end = i + 1;
 		while (end < edits.size()
 				&& (combineA(edits, end) || combineB(edits, end)))
 			end++;
 		return end - 1;
 	}
 
 	private boolean combineA(List<Edit> e, int i) {
 		return e.get(i).getBeginA() - e.get(i - 1).getEndA() <= 2 * context;
 	}
 
 	private boolean combineB(List<Edit> e, int i) {
 		return e.get(i).getBeginB() - e.get(i - 1).getEndB() <= 2 * context;
 	}
 
 	private static boolean end(Edit edit, int a, int b) {
 		return edit.getEndA() <= a && edit.getEndB() <= b;
 	}
 }