Fix Javadoc formatting of org.eclipse.jgit.diff package

Without explicit <p> elements, Javadoc joins all paragraph, resulting in
unreadable Javadoc output, e.g. see here:

http://download.eclipse.org/jgit/docs/jgit-2.1.0.201209190230-r/apidocs/org/eclipse/jgit/diff/MyersDiff.html

Also, <pre> is needed to preserve pre-formatted content.

The reflowing of text was automatically done on save.

Change-Id: Ia02dd6d759ae066700098e22669ef925e3c813b5

org.eclipse.jgit/src/org/eclipse/jgit/diff/ContentSource.java

@@ -64,7 +64,7 @@ import org.eclipse.jgit.treewalk.filter.PathFilter;
 
 /**
  * Supplies the content of a file for {@link DiffFormatter}.
- *
+ * <p>
  * A content source is not thread-safe. Sources may contain state, including
  * information about the last ObjectLoader they returned. Callers must be
  * careful to ensure there is no more than one ObjectLoader pending on any

org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java

@@ -45,7 +45,7 @@ package org.eclipse.jgit.diff;
 
 /**
  * Compares two {@link Sequence}s to create an {@link EditList} of changes.
- *
+ * <p>
  * An algorithm's {@code diff} method must be callable from concurrent threads
  * without data collisions. This permits some algorithms to use a singleton
  * pattern, with concurrent invocations using the same singleton. Other

org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequence.java

@@ -45,11 +45,11 @@ package org.eclipse.jgit.diff;
 
 /**
  * Wraps a {@link Sequence} to assign hash codes to elements.
- *
+ * <p>
  * This sequence acts as a proxy for the real sequence, caching element hash
  * codes so they don't need to be recomputed each time. Sequences of this type
  * must be used with a {@link HashedSequenceComparator}.
- *
+ * <p>
  * To construct an instance of this type use {@link HashedSequencePair}.
  *
  * @param <S>

org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequenceComparator.java

@@ -45,11 +45,11 @@ package org.eclipse.jgit.diff;
 
 /**
  * Wrap another comparator for use with {@link HashedSequence}.
- *
+ * <p>
  * This comparator acts as a proxy for the real comparator, evaluating the
  * cached hash code before testing the underlying comparator's equality.
  * Comparators of this type must be used with a {@link HashedSequence}.
- *
+ * <p>
  * To construct an instance of this type use {@link HashedSequencePair}.
  *
  * @param <S>

org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequencePair.java

@@ -45,7 +45,7 @@ package org.eclipse.jgit.diff;
 
 /**
  * Wraps two {@link Sequence} instances to cache their element hash codes.
- *
+ * <p>
  * This pair wraps two sequences that contain cached hash codes for the input
  * sequences.
  *

org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java

@@ -45,11 +45,11 @@ package org.eclipse.jgit.diff;
 
 /**
  * An extended form of Bram Cohen's patience diff algorithm.
- *
+ * <p>
  * 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>,
  * and then was further extended to support low-occurrence common elements.
- *
+ * <p>
  * The basic idea of the algorithm is to create a histogram of occurrences for
  * each element of sequence A. Each element of sequence B is then considered in
  * turn. If the element also exists in sequence A, and has a lower occurrence
@@ -58,34 +58,34 @@ package org.eclipse.jgit.diff;
  * lowest number of occurrences is chosen as a split point. The region is split
  * around the LCS, and the algorithm is recursively applied to the sections
  * before and after the LCS.
- *
+ * <p>
  * By always selecting a LCS position with the lowest occurrence count, this
  * algorithm behaves exactly like Bram Cohen's patience diff whenever there is a
  * unique common element available between the two sequences. When no unique
  * elements exist, the lowest occurrence element is chosen instead. This offers
  * more readable diffs than simply falling back on the standard Myers' O(ND)
  * algorithm would produce.
- *
+ * <p>
  * To prevent the algorithm from having an O(N^2) running time, an upper limit
  * on the number of unique elements in a histogram bucket is configured by
  * {@link #setMaxChainLength(int)}. If sequence A has more than this many
  * elements that hash into the same hash bucket, the algorithm passes the region
  * to {@link #setFallbackAlgorithm(DiffAlgorithm)}. If no fallback algorithm is
  * configured, the region is emitted as a replace edit.
- *
+ * <p>
  * During scanning of sequence B, any element of A that occurs more than
  * {@link #setMaxChainLength(int)} times is never considered for an LCS match
  * position, even if it is common between the two sequences. This limits the
  * number of locations in sequence A that must be considered to find the LCS,
  * and helps maintain a lower running time bound.
- *
+ * <p>
  * So long as {@link #setMaxChainLength(int)} is a small constant (such as 64),
  * the algorithm runs in O(N * D) time, where N is the sum of the input lengths
  * and D is the number of edits in the resulting EditList. If the supplied
  * {@link SequenceComparator} has a good hash function, this implementation
  * typically out-performs {@link MyersDiff}, even though its theoretical running
  * time is the same.
- *
+ * <p>
  * This implementation has an internal limitation that prevents it from handling
  * sequences with more than 268,435,456 (2^28) elements.
  */

org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiffIndex.java

@@ -47,7 +47,7 @@ import org.eclipse.jgit.internal.JGitText;
 
 /**
  * Support {@link HistogramDiff} by computing occurrence counts of elements.
- *
+ * <p>
  * Each element in the range being considered is put into a hash table, tracking
  * the number of times that distinct element appears in the sequence. Once all
  * elements have been inserted from sequence A, each element of sequence B is

org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java

@@ -51,56 +51,60 @@ import org.eclipse.jgit.util.IntList;
 import org.eclipse.jgit.util.LongList;
 
 /**
- * Diff algorithm, based on "An O(ND) Difference Algorithm and its
+ * Diff algorithm, based on "An O(ND) Difference Algorithm and its Variations",
- * Variations", by Eugene Myers.
+ * by Eugene Myers.
- *
+ * <p>
  * The basic idea is to put the line numbers of text A as columns ("x") and the
- * lines of text B as rows ("y").  Now you try to find the shortest "edit path"
+ * lines of text B as rows ("y"). Now you try to find the shortest "edit path"
- * from the upper left corner to the lower right corner, where you can
+ * from the upper left corner to the lower right corner, where you can always go
- * always go horizontally or vertically, but diagonally from (x,y) to
+ * horizontally or vertically, but diagonally from (x,y) to (x+1,y+1) only if
- * (x+1,y+1) only if line x in text A is identical to line y in text B.
+ * line x in text A is identical to line y in text B.
- *
+ * <p>
- * Myers' fundamental concept is the "furthest reaching D-path on diagonal k":
+ * Myers' fundamental concept is the "furthest reaching D-path on diagonal k": a
- * a D-path is an edit path starting at the upper left corner and containing
+ * D-path is an edit path starting at the upper left corner and containing
- * exactly D non-diagonal elements ("differences").  The furthest reaching
+ * exactly D non-diagonal elements ("differences"). The furthest reaching D-path
- * D-path on diagonal k is the one that contains the most (diagonal) elements
+ * on diagonal k is the one that contains the most (diagonal) elements which
- * which ends on diagonal k (where k = y - x).
+ * ends on diagonal k (where k = y - x).
- *
+ * <p>
  * Example:
  *
+ * <pre>
  *    H E L L O   W O R L D
  *    ____
  *  L     \___
  *  O         \___
  *  W             \________
- *
+ * </pre>
- * Since every D-path has exactly D horizontal or vertical elements, it can
+ * <p>
- * only end on the diagonals -D, -D+2, ..., D-2, D.
+ * Since every D-path has exactly D horizontal or vertical elements, it can only
- *
+ * end on the diagonals -D, -D+2, ..., D-2, D.
- * Since every furthest reaching D-path contains at least one furthest
+ * <p>
- * reaching (D-1)-path (except for D=0), we can construct them recursively.
+ * Since every furthest reaching D-path contains at least one furthest reaching
- *
+ * (D-1)-path (except for D=0), we can construct them recursively.
+ * <p>
  * Since we are really interested in the shortest edit path, we can start
  * looking for a 0-path, then a 1-path, and so on, until we find a path that
  * ends in the lower right corner.
- *
+ * <p>
  * To save space, we do not need to store all paths (which has quadratic space
- * requirements), but generate the D-paths simultaneously from both sides.
+ * requirements), but generate the D-paths simultaneously from both sides. When
- * When the ends meet, we will have found "the middle" of the path.  From the
+ * the ends meet, we will have found "the middle" of the path. From the end
- * end points of that diagonal part, we can generate the rest recursively.
+ * points of that diagonal part, we can generate the rest recursively.
- *
+ * <p>
  * This only requires linear space.
+ * <p>
+ * The overall (runtime) complexity is:
  *
- * The overall (runtime) complexity is
+ * <pre>
- *
+ *     O(N * D^2 + 2 * N/2 * (D/2)^2 + 4 * N/4 * (D/4)^2 + ...)
- *	O(N * D^2 + 2 * N/2 * (D/2)^2 + 4 * N/4 * (D/4)^2 + ...)
+ *     = O(N * D^2 * 5 / 4) = O(N * D^2),
- *	= O(N * D^2 * 5 / 4) = O(N * D^2),
+ * </pre>
- *
+ * <p>
- * (With each step, we have to find the middle parts of twice as many regions
+ * (With each step, we have to find the middle parts of twice as many regions as
- * as before, but the regions (as well as the D) are halved.)
+ * before, but the regions (as well as the D) are halved.)
- *
+ * <p>
- * So the overall runtime complexity stays the same with linear space,
+ * So the overall runtime complexity stays the same with linear space, albeit
- * albeit with a larger constant factor.
+ * with a larger constant factor.
  *
  * @param <S>
  *            type of sequence.

org.eclipse.jgit/src/org/eclipse/jgit/diff/Sequence.java

@@ -46,15 +46,15 @@ package org.eclipse.jgit.diff;
 
 /**
  * Arbitrary sequence of elements.
- *
+ * <p>
  * A sequence of elements is defined to contain elements in the index range
  * <code>[0, {@link #size()})</code>, like a standard Java List implementation.
  * Unlike a List, the members of the sequence are not directly obtainable.
- *
+ * <p>
  * Implementations of Sequence are primarily intended for use in content
  * difference detection algorithms, to produce an {@link EditList} of
  * {@link Edit} instances describing how two Sequence instances differ.
- *
+ * <p>
  * To be compared against another Sequence of the same type, a supporting
  * {@link SequenceComparator} must also be supplied.
  */

org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java

@@ -45,11 +45,11 @@ package org.eclipse.jgit.diff;
 
 /**
  * Equivalence function for a {@link Sequence} compared by difference algorithm.
- *
+ * <p>
  * Difference algorithms can use a comparator to compare portions of two
  * sequences and discover the minimal edits required to transform from one
  * sequence to the other sequence.
- *
+ * <p>
  * Indexes within a sequence are zero-based.
  *
  * @param <S>

org.eclipse.jgit/src/org/eclipse/jgit/diff/Subsequence.java

@@ -45,7 +45,7 @@ package org.eclipse.jgit.diff;
 
 /**
  * Wraps a {@link Sequence} to have a narrower range of elements.
- *
+ * <p>
  * This sequence acts as a proxy for the real sequence, translating element
  * indexes on the fly by adding {@code begin} to them. Sequences of this type
  * must be used with a {@link SubsequenceComparator}.
@@ -56,7 +56,7 @@ package org.eclipse.jgit.diff;
 public final class Subsequence<S extends Sequence> extends Sequence {
 	/**
 	 * Construct a subsequence around the A region/base sequence.
-	 * 
+	 *
 	 * @param <S>
 	 *            the base sequence type.
 	 * @param a
@@ -71,7 +71,7 @@ public final class Subsequence<S extends Sequence> extends Sequence {
 
 	/**
 	 * Construct a subsequence around the B region/base sequence.
-	 * 
+	 *
 	 * @param <S>
 	 *            the base sequence type.
 	 * @param b
@@ -86,7 +86,7 @@ public final class Subsequence<S extends Sequence> extends Sequence {
 
 	/**
 	 * Adjust the Edit to reflect positions in the base sequence.
-	 * 
+	 *
 	 * @param <S>
 	 *            the base sequence type.
 	 * @param e

org.eclipse.jgit/src/org/eclipse/jgit/diff/SubsequenceComparator.java

@@ -45,7 +45,7 @@ package org.eclipse.jgit.diff;
 
 /**
  * Wrap another comparator for use with {@link Subsequence}.
- *
+ * <p>
  * This comparator acts as a proxy for the real comparator, translating element
  * indexes on the fly by adding the subsequence's begin offset to them.
  * Comparators of this type must be used with a {@link Subsequence}.