Implement Bram Cohen's Patience Diff

Change-Id: Ic7a76df2861ea6c569ab9756a62018987912bd13 Signed-off-by: Shawn O. Pearce <spearce@spearce.org>
14 years ago · a67afbfee1
4 changed files with 925 additions and 0 deletions
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/PatienceDiffTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/PatienceDiffTest.java
@ -0,0 +1,231 @@
 /*
 * Copyright (C) 2010, Google Inc.
 * 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 java.io.UnsupportedEncodingException;
 import junit.framework.TestCase;
 public class PatienceDiffTest extends TestCase {
 	public void testEmptyInputs() {
 		EditList r = diff(t(""), t(""));
 		assertTrue("is empty", r.isEmpty());
 	}
 	public void testCreateFile() {
 		EditList r = diff(t(""), t("AB"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(0, 0, 0, 2), r.get(0));
 	}
 	public void testDeleteFile() {
 		EditList r = diff(t("AB"), t(""));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(0, 2, 0, 0), r.get(0));
 	}
 	public void testDegenerate_InsertMiddle() {
 		EditList r = diff(t("ac"), t("aBc"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(1, 1, 1, 2), r.get(0));
 	}
 	public void testDegenerate_DeleteMiddle() {
 		EditList r = diff(t("aBc"), t("ac"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(1, 2, 1, 1), r.get(0));
 	}
 	public void testDegenerate_ReplaceMiddle() {
 		EditList r = diff(t("bCd"), t("bEd"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(1, 2, 1, 2), r.get(0));
 	}
 	public void testDegenerate_InsertsIntoMidPosition() {
 		EditList r = diff(t("aaaa"), t("aaXaa"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(2, 2, 2, 3), r.get(0));
 	}
 	public void testDegenerate_InsertStart() {
 		EditList r = diff(t("bc"), t("Abc"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(0, 0, 0, 1), r.get(0));
 	}
 	public void testDegenerate_DeleteStart() {
 		EditList r = diff(t("Abc"), t("bc"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(0, 1, 0, 0), r.get(0));
 	}
 	public void testDegenerate_InsertEnd() {
 		EditList r = diff(t("bc"), t("bcD"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(2, 2, 2, 3), r.get(0));
 	}
 	public void testDegenerate_DeleteEnd() {
 		EditList r = diff(t("bcD"), t("bc"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(2, 3, 2, 2), r.get(0));
 	}
 	public void testEdit_ReplaceCommonDelete() {
 		EditList r = diff(t("RbC"), t("Sb"));
 		assertEquals(2, r.size());
 		assertEquals(new Edit(0, 1, 0, 1), r.get(0));
 		assertEquals(new Edit(2, 3, 2, 2), r.get(1));
 	}
 	public void testEdit_CommonReplaceCommonDeleteCommon() {
 		EditList r = diff(t("aRbCd"), t("aSbd"));
 		assertEquals(2, r.size());
 		assertEquals(new Edit(1, 2, 1, 2), r.get(0));
 		assertEquals(new Edit(3, 4, 3, 3), r.get(1));
 	}
 	public void testEdit_MoveBlock() {
 		EditList r = diff(t("aYYbcdz"), t("abcdYYz"));
 		assertEquals(2, r.size());
 		assertEquals(new Edit(1, 3, 1, 1), r.get(0));
 		assertEquals(new Edit(6, 6, 4, 6), r.get(1));
 	}
 	public void testEdit_InvertBlocks() {
 		EditList r = diff(t("aYYbcdXXz"), t("aXXbcdYYz"));
 		assertEquals(2, r.size());
 		assertEquals(new Edit(1, 3, 1, 3), r.get(0));
 		assertEquals(new Edit(6, 8, 6, 8), r.get(1));
 	}
 	public void testEdit_NoUniqueMiddleSideA() {
 		EditList r = diff(t("aRRSSz"), t("aSSRRz"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(1, 5, 1, 5), r.get(0));
 	}
 	public void testEdit_NoUniqueMiddleSideB() {
 		EditList r = diff(t("aRSz"), t("aSSRRz"));
 		assertEquals(1, r.size());
 		assertEquals(new Edit(1, 3, 1, 5), r.get(0));
 	}
 	public void testEdit_UniqueCommonLargerThanMatchPoint() {
 		// We are testing 3 unique common matches, but two of
 		// them are consumed as part of the 1st's LCS region.
 		EditList r = diff(t("AbdeZ"), t("PbdeQR"));
 		assertEquals(2, r.size());
 		assertEquals(new Edit(0, 1, 0, 1), r.get(0));
 		assertEquals(new Edit(4, 5, 4, 6), r.get(1));
 	}
 	public void testEdit_CommonGrowsPrefixAndSuffix() {
 		// Here there is only one common unique point, but we can grow it
 		// in both directions to find the LCS in the middle.
 		EditList r = diff(t("AaabccZ"), t("PaabccR"));
 		assertEquals(2, r.size());
 		assertEquals(new Edit(0, 1, 0, 1), r.get(0));
 		assertEquals(new Edit(6, 7, 6, 7), r.get(1));
 	}
 	public void testEdit_DuplicateAButCommonUniqueInB() {
 		EditList r = diff(t("AbbcR"), t("CbcS"));
 		assertEquals(2, r.size());
 		assertEquals(new Edit(0, 2, 0, 1), r.get(0));
 		assertEquals(new Edit(4, 5, 3, 4), r.get(1));
 	}
 	public void testPerformanceTestDeltaLength() {
 		String a = DiffTestDataGenerator.generateSequence(40000, 971, 3);
 		String b = DiffTestDataGenerator.generateSequence(40000, 1621, 5);
 		CharArray ac = new CharArray(a);
 		CharArray bc = new CharArray(b);
 		EditList r = new PatienceDiff().diff(new CharCmp(), ac, bc);
 		assertEquals(25, r.size());
 	}
 	private static EditList diff(RawText a, RawText b) {
 		return new PatienceDiff().diff(RawTextComparator.DEFAULT, a, b);
 	}
 	private static RawText t(String text) {
 		StringBuilder r = new StringBuilder();
 		for (int i = 0; i < text.length(); i++) {
 			r.append(text.charAt(i));
 			r.append('\n');
 		}
 		try {
 			return new RawText(r.toString().getBytes("UTF-8"));
 		} catch (UnsupportedEncodingException e) {
 			throw new RuntimeException(e);
 		}
 	}
 	private static class CharArray extends Sequence {
 		final char[] array;
 		public CharArray(String s) {
 			array = s.toCharArray();
 		}
 		@Override
 		public int size() {
 			return array.length;
 		}
 	}
 	private static class CharCmp extends SequenceComparator<CharArray> {
 		@Override
 		public boolean equals(CharArray a, int ai, CharArray b, int bi) {
 			return a.array[ai] == b.array[bi];
 		}
 		@Override
 		public int hash(CharArray seq, int ptr) {
 			return seq.array[ptr];
 		}
 	}
 }
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatienceDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatienceDiff.java
@ -0,0 +1,215 @@
 /*
 * Copyright (C) 2010, Google Inc.
 * 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;
 /**
 * An implementation of the patience difference algorithm.
 *
 * This implementation was derived by using the 4 rules that are outlined in
 * Bram Cohen's <a href="http://bramcohen.livejournal.com/73318.html">blog</a>.
 *
 * Because this algorithm requires finding a unique common point to center the
 * longest common subsequence around, input sequences which have no unique
 * elements create a degenerate Edit that simply replaces all of one sequence
 * with all of the other sequence. For many source code files and other human
 * maintained text, this isn't likely to occur. When it does occur, it can be
 * easier to read the resulting large-scale replace than to navigate through a
 * lot of slices of common-but-not-unique lines, like curly braces on lone
 * lines, or XML close tags. Consequently this algorithm is willing to create a
 * degenerate Edit in the worst case, in exchange for what may still be
 * perceived to be an easier to read patch script.
 *
 * In a nutshell, the implementation defines an Edit that replaces all of
 * sequence {@code a} with all of {@code b}. This Edit is reduced and/or split
 * to remove common elements, until only Edits spanning non-common elements
 * remain. Those {@link Edit}s are the differences.
 *
 * A slightly more detailed description of the implementation is:
 *
 * <ol>
 * <li>Define an Edit that spans the entire two sequences. This edit replaces
 * all of {@code a} with all of {@code b}.</li>
 *
 * <li>Shrink the Edit by shifting the starting points later in the sequence to
 * skip over any elements that are common between {@code a} and {@code b}.
 * Likewise shift the ending points earlier in the sequence to skip any trailing
 * elements that are common. The first and last element of the edit are now not
 * common, however there may be common content within the interior of the Edit
 * that hasn't been discovered yet.</li>
 *
 * <li>Find unique elements within the Edit region that are in both sequences.
 * This is currently accomplished by hashing the elements and merging them
 * through a custom hash table in {@link PatienceDiffIndex}.</li>
 *
 * <li>Order the common unique elements by their position within {@code b}.</li>
 *
 * <li>For each unique element, stretch an Edit around it in both directions,
 * consuming neighboring elements that are common to both sequences. Select the
 * longest such Edit out of the unique element list. During this stretching,
 * some subsequent unique elements may be consumed into an earlier's common
 * Edit. This means not all unique elements are evaluated.</li>
 *
 * <li>Split the Edit region at the longest common edit. Because step 2 shrank
 * the initial region, there must be at least one element before, and at least
 * one element after the split.</li>
 *
 * <li>Recurse on the before and after split points, starting from step 3. Step
 * 2 doesn't need to be done again because any common part was already removed
 * by the prior step 2 or 5.</li>
 * </ol>
 */
 public class PatienceDiff implements DiffAlgorithm {
 	/** Algorithm we use when there are no common unique lines in a region. */
 	private DiffAlgorithm fallback;
 	/**
 	 * Set the algorithm used when there are no common unique lines remaining.
 	 *
 	 * @param alg
 	 *            the secondary algorithm. If null the region will be denoted as
 	 *            a single REPLACE block.
 	 */
 	public void setFallbackAlgorithm(DiffAlgorithm alg) {
 		fallback = alg;
 	}
 	public <S extends Sequence, C extends SequenceComparator<? super S>> EditList diff(
 			C cmp, S a, S b) {
 		Edit region = new Edit(0, a.size(), 0, b.size());
 		region = cmp.reduceCommonStartEnd(a, b, region);
 		switch (region.getType()) {
 		case INSERT:
 		case DELETE: {
 			EditList r = new EditList();
 			r.add(region);
 			return r;
 		}
 		case REPLACE: {
 			SubsequenceComparator<S> cs = new SubsequenceComparator<S>(cmp);
 			Subsequence<S> as = Subsequence.a(a, region);
 			Subsequence<S> bs = Subsequence.b(b, region);
 			return Subsequence.toBase(diffImpl(cs, as, bs), as, bs);
 		}
 		case EMPTY:
 			return new EditList();
 		default:
 			throw new IllegalStateException();
 		}
 	}
 	private <S extends Sequence, C extends SequenceComparator<? super S>> EditList diffImpl(
 			C cmp, S a, S b) {
 		State<S> s = new State<S>(new HashedSequencePair<S>(cmp, a, b));
 		s.diff(new Edit(0, s.a.size(), 0, s.b.size()), null, 0, 0);
 		return s.edits;
 	}
 	private class State<S extends Sequence> {
 		private final HashedSequenceComparator<S> cmp;
 		private final HashedSequence<S> a;
 		private final HashedSequence<S> b;
 		/** Result edits we have determined that must be made to convert a to b. */
 		final EditList edits;
 		State(HashedSequencePair<S> p) {
 			this.cmp = p.getComparator();
 			this.a = p.getA();
 			this.b = p.getB();
 			this.edits = new EditList();
 		}
 		private void diff(Edit r, long[] pCommon, int pIdx, int pEnd) {
 			switch (r.getType()) {
 			case INSERT:
 			case DELETE:
 				edits.add(r);
 				return;
 			case REPLACE:
 				break;
 			case EMPTY:
 			default:
 				throw new IllegalStateException();
 			}
 			PatienceDiffIndex<S> p;
 			p = new PatienceDiffIndex<S>(cmp, a, b, r, pCommon, pIdx, pEnd);
 			Edit lcs = p.findLongestCommonSequence();
 			if (lcs != null) {
 				pCommon = p.nCommon;
 				pIdx = p.cIdx;
 				pEnd = p.nCnt;
 				p = null;
 				diff(r.before(lcs), pCommon, 0, pIdx);
 				diff(r.after(lcs), pCommon, pIdx + 1, pEnd);
 			} else if (fallback != null) {
 				p = null;
 				pCommon = null;
 				SubsequenceComparator<HashedSequence<S>> cs;
 				cs = new SubsequenceComparator<HashedSequence<S>>(cmp);
 				Subsequence<HashedSequence<S>> as = Subsequence.a(a, r);
 				Subsequence<HashedSequence<S>> bs = Subsequence.b(b, r);
 				EditList res = fallback.diff(cs, as, bs);
 				edits.addAll(Subsequence.toBase(res, as, bs));
 			} else {
 				edits.add(r);
 			}
 		}
 	}
 }
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatienceDiffIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatienceDiffIndex.java
@ -0,0 +1,442 @@
 /*
 * Copyright (C) 2010, Google Inc.
 * 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;
 /**
 * Supports {@link PatienceDiff} by finding unique but common elements.
 *
 * This index object is constructed once for each region being considered by the
 * main {@link PatienceDiff} algorithm, which really means its once for each
 * recursive step. Each index instance processes a fixed sized region from the
 * sequences, and during recursion the region is split into two smaller segments
 * and processed again.
 *
 * Index instances from a higher level invocation message some state into a
 * lower level invocation by passing the {@link #nCommon} array from the higher
 * invocation into the two sub-steps as {@link #pCommon}. This permits some
 * matching work that was already done in the higher invocation to be reused in
 * the sub-step and can save a lot of time when element equality is expensive.
 *
 * @param <S>
 *            type of sequence the scanner will scan.
 */
 final class PatienceDiffIndex<S extends Sequence> {
 	private static final int A_DUPLICATE = 1;
 	private static final int B_DUPLICATE = 2;
 	private static final int DUPLICATE_MASK = B_DUPLICATE | A_DUPLICATE;
 	private static final int A_SHIFT = 2;
 	private static final int B_SHIFT = 31 + 2;
 	private static final int PTR_MASK = 0x7fffffff;
 	private final HashedSequenceComparator<S> cmp;
 	private final HashedSequence<S> a;
 	private final HashedSequence<S> b;
 	private final Edit region;
 	/** Pairs of beginB, endB indices previously found to be common and unique. */
 	private final long[] pCommon;
 	/** First valid index in {@link #pCommon}. */
 	private final int pBegin;
 	/** 1 past the last valid entry in {@link #pCommon}. */
 	private final int pEnd;
 	/** Keyed by {@code cmp.hash() & tableMask} to yield an entry offset. */
 	private final int[] table;
 	private final int tableMask;
 	// To save memory the buckets for hash chains are stored in correlated
 	// arrays. This permits us to get 3 values per entry, without paying
 	// the penalty for an object header on each entry.
 	/** Cached hash value for an element as returned by {@link #cmp}. */
 	private final int[] hash;
 	/**
 	 * A matched (or partially examined) element from the two sequences.
 	 *
 	 * This is actually a 4-tuple: (bPtr, aPtrP1, bDuplicate, aDuplicate).
 	 *
 	 * bPtr and aPtr are each 31 bits. bPtr is exactly the position in the b
 	 * sequence, while aPtrP1 is {@code aPtr + 1}. This permits us to determine
 	 * if there is corresponding element in a by testing for aPtrP1 != 0. If it
 	 * equals 0, there is no element in a. If it equals 1, element 0 of a
 	 * matches with element bPtr of b.
 	 *
 	 * bDuplicate is 1 if this element occurs more than once in b; likewise
 	 * aDuplicate is 1 if this element occurs more than once in a. These flags
 	 * permit each element to only be added to the index once. As the duplicates
 	 * are the low 2 bits a unique record meets (@code (rec & 2) == 0}.
 	 */
 	private final long[] ptrs;
 	/** Array index of the next entry in the table; 0 if at end of chain. */
 	private final int[] next;
 	/** Total number of entries that exist in {@link #ptrs}. */
 	private int entryCnt;
 	/** Number of entries in {@link #ptrs} that are actually unique. */
 	private int uniqueCommonCnt;
 	/**
 	 * Pairs of beginB, endB indices found to be common and unique.
 	 *
 	 * In order to find the longest common (but unique) sequence within a
 	 * region, we also found all of the other common but unique sequences in
 	 * that same region. This array stores all of those results, allowing them
 	 * to be passed into the subsequent recursive passes so we can later reuse
 	 * these matches and avoid recomputing the same points again.
 	 */
 	long[] nCommon;
 	/** Number of items in {@link #nCommon}. */
 	int nCnt;
 	/** Index of the longest common subsequence in {@link #nCommon}. */
 	int cIdx;
 	PatienceDiffIndex(HashedSequenceComparator<S> cmp, //
 			HashedSequence<S> a, //
 			HashedSequence<S> b, //
 			Edit region, //
 			long[] pCommon, int pIdx, int pCnt) {
 		this.cmp = cmp;
 		this.a = a;
 		this.b = b;
 		this.region = region;
 		this.pCommon = pCommon;
 		this.pBegin = pIdx;
 		this.pEnd = pCnt;
 		final int blockCnt = region.getLengthB();
 		if (blockCnt < 1) {
 			table = new int[] {};
 			tableMask = 0;
 			hash = new int[] {};
 			ptrs = new long[] {};
 			next = new int[] {};
 		} else {
 			table = new int[tableSize(blockCnt)];
 			tableMask = table.length - 1;
 			// As we insert elements we preincrement so that 0 is never a
 			// valid entry. Therefore we have to allocate one extra space.
 			//
 			hash = new int[1 + blockCnt];
 			ptrs = new long[hash.length];
 			next = new int[hash.length];
 		}
 	}
 	/**
 	 * Index elements in sequence B for later matching with sequence A.
 	 *
 	 * This is the first stage of preparing an index to find the longest common
 	 * sequence. Elements of sequence B in the range [ptr, end) are scanned in
 	 * order and added to the internal hashtable.
 	 *
 	 * If prior matches were given in the constructor, these may be used to
 	 * fast-forward through sections of B to avoid unnecessary recomputation.
 	 */
 	private void scanB() {
 		// We insert in ascending order so that a later scan of the table
 		// from 0 through entryCnt will iterate through B in order. This
 		// is the desired result ordering from match().
 		//
 		int ptr = region.beginB;
 		final int end = region.endB;
 		int pIdx = pBegin;
 		SCAN: while (ptr < end) {
 			final int key = cmp.hash(b, ptr);
 			final int tIdx = key & tableMask;
 			if (pIdx < pEnd) {
 				final long priorRec = pCommon[pIdx];
 				if (ptr == bOf(priorRec)) {
 					// We know this region is unique from a prior pass.
 					// Insert the start point, and skip right to the end.
 					//
 					insertB(key, tIdx, ptr);
 					pIdx++;
 					ptr = aOfRaw(priorRec);
 					continue SCAN;
 				}
 			}
 			// We aren't sure what the status of this element is. Add
 			// it to our hashtable, and flag it as duplicate if there
 			// was already a different entry present.
 			//
 			for (int eIdx = table[tIdx]; eIdx != 0; eIdx = next[eIdx]) {
 				if (hash[eIdx] != key)
 					continue;
 				final long rec = ptrs[eIdx];
 				if (cmp.equals(b, ptr, b, bOf(rec))) {
 					ptrs[eIdx] = rec | B_DUPLICATE;
 					ptr++;
 					continue SCAN;
 				}
 			}
 			insertB(key, tIdx, ptr);
 			ptr++;
 		}
 	}
 	private void insertB(final int key, final int tIdx, int ptr) {
 		final int eIdx = ++entryCnt;
 		hash[eIdx] = key;
 		ptrs[eIdx] = ((long) ptr) << B_SHIFT;
 		next[eIdx] = table[tIdx];
 		table[tIdx] = eIdx;
 	}
 	/**
 	 * Index elements in sequence A for later matching.
 	 *
 	 * This is the second stage of preparing an index to find the longest common
 	 * sequence. The state requires {@link #scanB()} to have been invoked first.
 	 *
 	 * Each element of A in the range [ptr, end) are searched for in the
 	 * internal hashtable, to see if B has already registered a location.
 	 *
 	 * If prior matches were given in the constructor, these may be used to
 	 * fast-forward through sections of A to avoid unnecessary recomputation.
 	 */
 	private void scanA() {
 		int ptr = region.beginA;
 		final int end = region.endA;
 		int pLast = pBegin - 1;
 		SCAN: while (ptr < end) {
 			final int key = cmp.hash(a, ptr);
 			final int tIdx = key & tableMask;
 			for (int eIdx = table[tIdx]; eIdx != 0; eIdx = next[eIdx]) {
 				final long rec = ptrs[eIdx];
 				if (isDuplicate(rec) || hash[eIdx] != key)
 					continue;
 				final int aPtr = aOfRaw(rec);
 				if (aPtr != 0 && cmp.equals(a, ptr, a, aPtr - 1)) {
 					ptrs[eIdx] = rec | A_DUPLICATE;
 					uniqueCommonCnt--;
 					ptr++;
 					continue SCAN;
 				}
 				final int bs = bOf(rec);
 				if (!cmp.equals(a, ptr, b, bs)) {
 					ptr++;
 					continue SCAN;
 				}
 				// This element is both common and unique. Link the
 				// two sequences together at this point.
 				//
 				ptrs[eIdx] = rec | (((long) (ptr + 1)) << A_SHIFT);
 				uniqueCommonCnt++;
 				if (pBegin < pEnd) {
 					// If we have prior match point data, we might be able
 					// to locate the length of the match and skip past all
 					// of those elements. We try to take advantage of the
 					// fact that pCommon is sorted by B, and its likely that
 					// matches in A appear in the same order as they do in B.
 					//
 					for (int pIdx = pLast + 1;; pIdx++) {
 						if (pIdx == pEnd)
 							pIdx = pBegin;
 						else if (pIdx == pLast)
 							break;
 						final long priorRec = pCommon[pIdx];
 						final int priorB = bOf(priorRec);
 						if (bs < priorB)
 							break;
 						if (bs == priorB) {
 							ptr += aOfRaw(priorRec) - priorB;
 							pLast = pIdx;
 							continue SCAN;
 						}
 					}
 				}
 				ptr++;
 				continue SCAN;
 			}
 			ptr++;
 		}
 	}
 	/**
 	 * Scan all potential matches and find the longest common sequence.
 	 *
 	 * If this method returns non-null, the caller should copy out the
 	 * {@link #nCommon} array and pass that through to the recursive sub-steps
 	 * so that existing common matches can be reused rather than recomputed.
 	 *
 	 * @return an edit covering the longest common sequence. Null if there are
 	 *         no common unique sequences present.
 	 */
 	Edit findLongestCommonSequence() {
 		scanB();
 		scanA();
 		if (uniqueCommonCnt == 0)
 			return null;
 		nCommon = new long[uniqueCommonCnt];
 		int pIdx = pBegin;
 		Edit lcs = new Edit(0, 0);
 		MATCH: for (int eIdx = 1; eIdx <= entryCnt; eIdx++) {
 			final long rec = ptrs[eIdx];
 			if (isDuplicate(rec) || aOfRaw(rec) == 0)
 				continue;
 			int bs = bOf(rec);
 			if (bs < lcs.endB)
 				continue;
 			int as = aOf(rec);
 			if (pIdx < pEnd) {
 				final long priorRec = pCommon[pIdx];
 				if (bs == bOf(priorRec)) {
 					// We had a prior match and we know its unique.
 					// Reuse its region rather than computing again.
 					//
 					int be = aOfRaw(priorRec);
 					if (lcs.getLengthB() < be - bs) {
 						as -= bOf(rec) - bs;
 						lcs.beginA = as;
 						lcs.beginB = bs;
 						lcs.endA = as + (be - bs);
 						lcs.endB = be;
 						cIdx = nCnt;
 					}
 					nCommon[nCnt] = priorRec;
 					if (++nCnt == uniqueCommonCnt)
 						break MATCH;
 					pIdx++;
 					continue MATCH;
 				}
 			}
 			// We didn't have prior match data, or this is the first time
 			// seeing this particular pair. Extend the region as large as
 			// possible and remember it for future use.
 			//
 			int ae = as + 1;
 			int be = bs + 1;
 			while (region.beginA < as && region.beginB < bs
 					&& cmp.equals(a, as - 1, b, bs - 1)) {
 				as--;
 				bs--;
 			}
 			while (ae < region.endA && be < region.endB
 					&& cmp.equals(a, ae, b, be)) {
 				ae++;
 				be++;
 			}
 			if (lcs.getLengthB() < be - bs) {
 				lcs.beginA = as;
 				lcs.beginB = bs;
 				lcs.endA = ae;
 				lcs.endB = be;
 				cIdx = nCnt;
 			}
 			nCommon[nCnt] = (((long) bs) << B_SHIFT) | (((long) be) << A_SHIFT);
 			if (++nCnt == uniqueCommonCnt)
 				break MATCH;
 		}
 		return lcs;
 	}
 	private static boolean isDuplicate(long rec) {
 		return (((int) rec) & DUPLICATE_MASK) != 0;
 	}
 	private static int aOfRaw(long rec) {
 		return ((int) (rec >>> A_SHIFT)) & PTR_MASK;
 	}
 	private static int aOf(long rec) {
 		return aOfRaw(rec) - 1;
 	}
 	private static int bOf(long rec) {
 		return (int) (rec >>> B_SHIFT);
 	}
 	private static int tableSize(final int worstCaseBlockCnt) {
 		int shift = 32 - Integer.numberOfLeadingZeros(worstCaseBlockCnt);
 		int sz = 1 << (shift - 1);
 		if (sz < worstCaseBlockCnt)
 			sz <<= 1;
 		return sz;
 	}
 }
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
@ -92,4 +92,41 @@ public abstract class SequenceComparator<S extends Sequence> {
 	 * @return hash the hash value.
 	 */
 	public abstract int hash(S seq, int ptr);
 	/**
 	 * Modify the edit to remove common leading and trailing items.
 	 *
 	 * The supplied edit {@code e} is reduced in size by moving the beginning A
 	 * and B points so the edit does not cover any items that are in common
 	 * between the two sequences. The ending A and B points are also shifted to
 	 * remove common items from the end of the region.
 	 *
 	 * @param a
 	 *            the first sequence.
 	 * @param b
 	 *            the second sequence.
 	 * @param e
 	 *            the edit to start with and update.
 	 * @return {@code e} if it was updated in-place, otherwise a new edit
 	 *         containing the reduced region.
 	 */
 	public Edit reduceCommonStartEnd(S a, S b, Edit e) {
 		// Skip over items that are common at the start.
 		//
 		while (e.beginA < e.endA && e.beginB < e.endB
 				&& equals(a, e.beginA, b, e.beginB)) {
 			e.beginA++;
 			e.beginB++;
 		}
 		// Skip over items that are common at the end.
 		//
 		while (e.beginA < e.endA && e.beginB < e.endB
 				&& equals(a, e.endA - 1, b, e.endB - 1)) {
 			e.endA--;
 			e.endB--;
 		}
 		return e;
 	}
 }