org.abego.commons.diff.internal.SequenceDiffDefault Maven / Gradle / Ivy
/*
* MIT License
*
* Copyright (c) 2020 Udo Borkowski, ([email protected])
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/
package org.abego.commons.diff.internal;
import org.abego.commons.seq.Seq;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import static org.abego.commons.diff.internal.AlignedItemPair.newAlignedItemPair;
import static org.abego.commons.lang.CharacterUtil.NEWLINE_CHAR;
import static org.abego.commons.lang.CharacterUtil.TAB_CHAR;
import static org.abego.commons.seq.SeqUtil.newSeq;
/**
* Provides a implementation for the SequenceDiff interface using a dynamic
* programming algorithm to compute edit distances.
*
* The algorithm has a time and space complexity of O(n*m).
*
* For details see:
*
* Dan Gusfield - Algorithms on Strings, Trees and Sequences;
* Cambridge University Press, 1999; pp. 215
*
*/
final class SequenceDiffDefault implements SequenceDiff {
private static final int MOVE_UP_MASK = 0x01;
private static final int MOVE_LEFT_MASK = 0x02;
private static final int MOVE_DIAGONAL_MASK = 0x04;
// package private for tests
static String tableToString(
Object[][] table,
Seq sequence1,
Seq sequence2) {
char colSeparator = TAB_CHAR;
StringBuilder sb = new StringBuilder();
sb.append(colSeparator);
for (T o : sequence1) {
sb.append(colSeparator);
sb.append(o);
}
for (int i2 = 0; i2 <= sequence2.size(); i2++) {
sb.append(NEWLINE_CHAR);
if (i2 > 0) {
sb.append(sequence2.item(i2 - 1));
}
for (int i1 = 0; i1 <= sequence1.size(); i1++) {
sb.append(colSeparator);
sb.append(table[i1][i2]);
}
}
return sb.toString();
}
public Seq> alignItems(
Seq sequenceA,
Seq sequenceB) {
List> result = new ArrayList<>();
Item[][] table = calcEditDistanceTable(sequenceA, sequenceB);
int i1 = sequenceA.size();
int i2 = sequenceB.size();
while (i1 > 0 || i2 > 0) {
// Determine the move to make.
// First check if a preferred move is defined. If not use the
// "normal" one
int move = table[i1][i2].getPreferredMove();
if (move == 0) {
move = table[i1][i2].getMoveMask();
}
// Create the proper result pair, based on the move.
if ((move & MOVE_DIAGONAL_MASK) != 0) {
result.add(0, newAlignedItemPair(
sequenceA.item(i1 - 1),
sequenceB.item(i2 - 1)));
i1--;
i2--;
} else if ((move & MOVE_LEFT_MASK) != 0) {
result.add(0, newAlignedItemPair(sequenceA.item(i1 - 1), null));
i1--;
} else {
result.add(0, newAlignedItemPair(null, sequenceB.item(i2 - 1)));
i2--;
}
}
return newSeq(result);
}
Item[][] calcEditDistanceTable(
Seq sequence1,
Seq sequence2) {
int sequence1Len = sequence1.size();
int sequence2Len = sequence2.size();
Item[][] table = new Item[sequence1Len + 1][sequence2Len + 1];
// Fill the first column/row
table[0][0] = new Item(0, 0, 0, 0);
for (int i1 = 1; i1 <= sequence1Len; i1++) {
table[i1][0] = new Item(
i1,
MOVE_LEFT_MASK,
0,
MOVE_LEFT_MASK);
}
for (int i2 = 0; i2 <= sequence2Len; i2++) {
table[0][i2] = new Item(
i2,
MOVE_UP_MASK,
0,
MOVE_UP_MASK);
}
for (int i1 = 1; i1 <= sequence1Len; i1++) {
for (int i2 = 1; i2 <= sequence2Len; i2++) {
boolean matched = Objects.equals(
sequence1.item(i1 - 1),
sequence2.item(i2 - 1));
int effortLeft = table[i1 - 1][i2].getEffort();
int effortUp = table[i1][i2 - 1].getEffort();
int effortDiag = table[i1 - 1][i2 - 1].getEffort();
int t = matched ? 0 : 1;
int newEffort = Math.min(effortDiag + t, Math.min(
effortLeft + 1,
effortUp + 1));
int moveMask = 0;
int matchCount = 0;
int preferredMove = 0;
if (newEffort == effortUp + 1) {
moveMask |= MOVE_UP_MASK;
int aMatchCount = table[i1][i2 - 1]
.getMatchCount();
if (matchCount < aMatchCount) {
matchCount = aMatchCount;
preferredMove = MOVE_UP_MASK;
}
}
if (newEffort == effortLeft + 1) {
moveMask |= MOVE_LEFT_MASK;
int aMatchCount = table[i1 - 1][i2]
.getMatchCount();
if (matchCount < aMatchCount) {
matchCount = aMatchCount;
preferredMove = MOVE_LEFT_MASK;
}
}
if (newEffort == effortDiag + t) {
moveMask |= MOVE_DIAGONAL_MASK;
int aMatchCount = table[i1 - 1][i2 - 1]
.getMatchCount();
if (matchCount < aMatchCount) {
matchCount = aMatchCount;
preferredMove = MOVE_DIAGONAL_MASK;
}
}
if (matched) {
matchCount++;
}
table[i1][i2] = new Item(
newEffort,
moveMask,
matchCount,
preferredMove);
}
}
return table;
}
static class Item {
private final int effort;
private final int moveMask;
private final int matchCount;
private final int preferredMove;
public Item(
int effort,
int moveMask,
int matchCount,
int preferredMove) {
this.effort = effort;
this.moveMask = moveMask;
this.matchCount = matchCount;
this.preferredMove = preferredMove;
}
@SuppressWarnings("MagicCharacter")
private static String getMoveMaskString(int mask) {
String result = ""; //$NON-NLS-1$
if ((mask & MOVE_LEFT_MASK) != 0) {
result += '-';
}
if ((mask & MOVE_DIAGONAL_MASK) != 0) {
result += '\\';
}
if ((mask & MOVE_UP_MASK) != 0) {
result += '|';
}
return result;
}
public int getEffort() {
return effort;
}
public int getMatchCount() {
return matchCount;
}
public int getMoveMask() {
return moveMask;
}
public String toString() {
return String.format("%s[%d;%d%s]", //NON-NLS
getMoveMaskString(moveMask),
effort,
matchCount,
getMoveMaskString(preferredMove));
}
public int getPreferredMove() {
return preferredMove;
}
}
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