2
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What's the fastest (quality is important too, but a little less important) way to compare two strings?

I'm looking for the most efficient way to compare two strings. Some of the strings I'm comparing can be over 5000 characters long. I'm comparing a list of about 80 strings with another list of about 200 strings. It takes forever, even when I'm threading it.

I'm using the StringUtils.getLevenshteinDistance(String s, String t) method from Apache Commons. My method follows. Is there a better way to do this?

private void compareMe() {
  List<String> compareStrings = MainController.getInstance().getCompareStrings();
  for (String compare : compareStrings) {
    int levenshteinDistance = StringUtils.getLevenshteinDistance(me, compare, bestScore); //bestScore begins at 999999999 :)
    if (bestScore > levenshteinDistance
          && levenshteinDistance > -1) {
      bestScore = levenshteinDistance; //global variable
      bestString = compare; //global variable
    }
  }
}

Here's a sample of two strings which should have a good score:

String 1:

SELECT 
CORP_VENDOR_NAME as "Corporate Vendor Name",
CORP_VENDOR_REF_ID as "Reference ID",
MERCHANT_ID as "Merchant ID",
VENDOR_CITY as "City",
VENDOR_STATE as "State",
VENDOR_ZIP as "Zip",
VENDOR_COUNTRY as "Country",
REMIT_VENDOR_NAME as "Remit Name",
REMIT_VENDOR_REF_ID as " Remit Reference ID",
VENDOR_PRI_UNSPSC_CODE as "Primary UNSPSC"
FROM DSS_FIN_USER.ACQ_VENDOR_DIM
WHERE VENDOR_REFERENCE_ID in 
(SELECT distinct CORP_VENDOR_REF_ID
FROM DSS_FIN_USER.ACQ_VENDOR_DIM
WHERE CORP_VENDOR_REF_ID = '${request.corp_vendor_id};')

String 2:

SELECT 
CORP_VENDOR_NAME as "Corporate Vendor Name",
CORP_VENDOR_REF_ID as "Reference ID",
MERCHANT_ID as "Merchant ID",
VENDOR_CITY as "City",
VENDOR_STATE as "State",
VENDOR_ZIP as "Zip",
VENDOR_COUNTRY as "Country",
REMIT_VENDOR_NAME as "Remit Name",
REMIT_VENDOR_REF_ID as " Remit Reference ID",
VENDOR_PRI_UNSPSC_CODE as "Primary UNSPSC"
FROM DSS_FIN_USER.ACQ_VENDOR_DIM
WHERE VENDOR_REFERENCE_ID in 
(SELECT distinct CORP_VENDOR_REF_ID
FROM DSS_FIN_USER.ACQ_VENDOR_DIM
WHERE CORP_VENDOR_REF_ID = 'ACQ-169013')

You'll notice the only difference is the '${request.corp_vendor_id};' at the end of the string. This would cause it to have a score of 26.

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  • 2
    \$\begingroup\$ If you really need to compare 80 strings with 200 strings for a total of 80*200 = 10000 comparisons, I see no way around it (try to use C?). But are you sure you need to do that all in one go? What problem are you trying to solve? \$\endgroup\$ – Andres Riofrio May 24 '12 at 20:03
  • \$\begingroup\$ Do you need to calculate the score or looking for exact match is enough? \$\endgroup\$ – Zecas May 24 '12 at 20:32
  • \$\begingroup\$ I need the closest match. \$\endgroup\$ – kentcdodds May 24 '12 at 20:52
  • \$\begingroup\$ Is Levenshtein the only algorithm you can use? \$\endgroup\$ – jasonk May 24 '12 at 21:52
  • 1
    \$\begingroup\$ Comparing two strings of 10 and 100 characters Levensthein does a full evaluation, but one can easily short cut the evaluation above some threshhold, say distance > 10, and do some heuristics like difference in string length. \$\endgroup\$ – Joop Eggen May 25 '12 at 20:44
2
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A possible suggestions. By looking at your data, I see that the difference between the strings may be small.

Since Levenshtein distance is a costly metric, it may be profitable to compute some other easy metric such that it is not too different from what may be obtained from Levenshtein metric, and use it to presort the arrays.

Once you have presorted them, merge the arrays together, and find the neighbors with in a delta range. For these, you can compute the Levenshtein distance and verify.

Possible metrics to use for pre-sorting include

  • frequency count of letters,
  • string length
  • lexicographical ordering

etc.

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3
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The painless solutiuon is to use the fastest levenstein distance algorithm :) For example extracted from GWT! I've created two 5 KB strings using your example, load them and produce 16000 calculations. Done in 3 seconds only. The source:

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;

public class Main {

private static String readString(String filename) throws IOException {
    StringBuilder result = new StringBuilder();
    String temp;
    BufferedReader in = new BufferedReader(new FileReader(filename));
    while ((temp = in.readLine()) != null) result.append(temp);
    return result.toString();
}

public static void main(String[] args) throws IOException {

    String line1 = readString(args[0]);
    String line2 = readString(args[1]);
    GeneralEditDistance ed = GeneralEditDistances.getLevenshteinDistance(line1);

    long time = System.currentTimeMillis();
    int best = Integer.MAX_VALUE;
    for (int i = 0; i < 80*200; i++) {
        best = Math.min(best, ed.getDistance(line2, best));
    }
    System.out.println("Best distance = " + best + " Total time (ms): " + (System.currentTimeMillis() - time));
}}

abstract class CharIndex {

static class FullHash extends CharIndex {

    static class Char {
        char c;

        @Override
        public boolean equals(Object x) {
            return (x != null) && (((Char) x).c == this.c);
        }

        @Override
        public int hashCode() {
            return c;
        }

        @Override
        public String toString() {
            return "'" + c + "'";
        }
    }

    static final int NULL_ELEMENT = 0;
    protected int lastUsed = NULL_ELEMENT;
    final java.util.HashMap<Char, Integer> map;

    FullHash(CharSequence s) {
        int len = s.length();
        int power = Integer.highestOneBit(len);

        map = new java.util.HashMap<Char, Integer>(
                power << ((power == len) ? 1 : 2));

        Char test = new Char();                   /* (re)used for lookup */
        for (int i = 0; i < s.length(); i++) {
            test.c = s.charAt(i);
            if (map.get(test) == null) {
                map.put(test, new Integer(++lastUsed));
                test = new Char();
            }
        }
    }

    @Override
    public int lookup(char c) {
        final Char lookupTest = new Char();
        lookupTest.c = c;
        Integer result = map.get(lookupTest);
        return (result != null) ? result.intValue() : 0;
    }

    @Override
    public int[] map(CharSequence s, int[] mapped) {
        /* Create one mutable Char, and reuse it for all lookups */
        final Char lookupTest = new Char();

        int len = s.length();
        if (mapped.length < len) {
            mapped = new int[len];
        }

        for (int i = 0; i < len; i++) {
            lookupTest.c = s.charAt(i);
            Integer result = map.get(lookupTest);
            mapped[i] = (result != null) ? result.intValue() : NULL_ELEMENT;
        }
        return mapped;
    }

    @Override
    public int nullElement() {
        return NULL_ELEMENT;
    }

    @Override
    public int size() {
        return lastUsed + 1;
    }
}

static class Masked extends CharIndex {
    static final int SIZE = 0x100;
    static final int MASK = (SIZE - 1);
    static final int NULL_ELEMENT = SIZE;

    static Masked generate(CharSequence s) {
        char[] contains = new char[SIZE];
        contains[0] = (char) 1;
        for (int i = 0; i < s.length(); i++) {
            char c = s.charAt(i);
            int index = c & MASK;
            if (contains[index] != c) {
                if ((contains[index] & MASK) == index) {
                    return null;
                }
                contains[index] = c;
            }
        }
        return new Masked(contains);
    }

    final char[] contains;

    private Masked(char[] contains) {
        this.contains = contains;
    }

    @Override
    public int lookup(char c) {
        int index = c & MASK;
        return (c == contains[index]) ? index : NULL_ELEMENT;
    }

    @Override
    public int[] map(CharSequence s, int[] mapped) {
        int len = s.length();
        if (mapped.length < len) {
            mapped = new int[len];
        }
        for (int i = 0; i < len; i++) {
            char c = s.charAt(i);
            int index = c & MASK;
            mapped[i] = (c == contains[index]) ? index : NULL_ELEMENT;
        }
        return mapped;
    }

    @Override
    public int nullElement() {
        return NULL_ELEMENT;
    }

    @Override
    public int size() {
        return NULL_ELEMENT + 1;
    }
}

static class Straight extends CharIndex {
    static final int MAX = 0x80;
    static final int MASK = ~(MAX - 1);
    static final int NULL_ELEMENT = MAX;

    static Straight generate(CharSequence s) {
        for (int i = 0; i < s.length(); i++) {
            if ((s.charAt(i) & MASK) != 0) {
                return null;
            }
        }

        return new Straight();
    }

    private Straight() {
    }

    @Override
    public int lookup(char c) {
        return ((c & MASK) == 0) ? c : NULL_ELEMENT;
    }

    @Override
    public int[] map(CharSequence s, int[] mapped) {
        int len = s.length();
        if (mapped.length < len) {
            mapped = new int[len];
        }
        for (int i = 0; i < len; i++) {
            char c = s.charAt(i);
            mapped[i] = ((c & MASK) == 0) ? c : NULL_ELEMENT;
        }
        return mapped;
    }

    @Override
    public int nullElement() {
        return NULL_ELEMENT;
    }

    @Override
    public int size() {
        return NULL_ELEMENT + 1;
    }
}

public static CharIndex getInstance(CharSequence s) {
    CharIndex result;

    if ((result = Straight.generate(s)) != null) {
        return result;
    }

    if ((result = Masked.generate(s)) != null) {
        return result;
    }

    return new FullHash(s);
}

public abstract int lookup(char c);

public abstract int[] map(CharSequence s, int[] mapped);

public abstract int nullElement();

public abstract int size();
}


interface GeneralEditDistance {

GeneralEditDistance duplicate();

int getDistance(CharSequence target, int limit);

}


class GeneralEditDistances {

private static class Levenshtein implements GeneralEditDistance {
    private ModifiedBerghelRoachEditDistance berghel;
    private MyersBitParallelEditDistance myers;
    private final CharSequence pattern;
    private final int patternLength;

    private Levenshtein(CharSequence pattern) {
        this.pattern = pattern;
        this.patternLength = pattern.length();
    }

    public GeneralEditDistance duplicate() {
        Levenshtein dup = new Levenshtein(pattern);
        if (this.myers != null) {
            dup.myers = (MyersBitParallelEditDistance) this.myers.duplicate();
        }
        return dup;
    }

    public int getDistance(CharSequence target, int limit) {
        if (limit <= 1) {
            return limit == 0 ?
                    (pattern.equals(target) ? 0 : 1) :
                    atMostOneError(pattern, target);
        }
        if ((patternLength > 64)
                && (limit < (target.length() / 10))) {
            if (berghel == null) {
                berghel = ModifiedBerghelRoachEditDistance.getInstance(pattern);
            }
            return berghel.getDistance(target, limit);
        }

        if (myers == null) {
            myers = MyersBitParallelEditDistance.getInstance(pattern);
        }

        return myers.getDistance(target, limit);
    }
}

public static int atMostOneError(CharSequence s1, CharSequence s2) {
    int s1Length = s1.length();
    int s2Length = s2.length();
    int errors = 0;             /* running count of edits required */

    switch (s2Length - s1Length) {
        /*
        * Strings are the same length.  No single insert/delete is possible;
        * at most one substitution can be present.
        */
        case 0:
            for (int i = 0; i < s2Length; i++) {
                if ((s2.charAt(i) != s1.charAt(i)) && (errors++ != 0)) {
                    break;
                }
            }
            return errors;

        case 1: /* s2Length > s1Length */
            for (int i = 0; i < s1Length; i++) {
                if (s2.charAt(i) != s1.charAt(i)) {
                    for (; i < s1Length; i++) {
                        if (s2.charAt(i + 1) != s1.charAt(i)) {
                            return 2;
                        }
                    }
                    return 1;
                }
            }
            return 1;

        /* Same as above case, with strings reversed */
        case -1: /* s1Length > s2Length */
            for (int i = 0; i < s2Length; i++) {
                if (s2.charAt(i) != s1.charAt(i)) {
                    for (; i < s2Length; i++) {
                        if (s2.charAt(i) != s1.charAt(i + 1)) {
                            return 2;
                        }
                    }
                    return 1;
                }
            }
            return 1;

        /* Edit distance is at least difference in lengths; more than 1 here. */
        default:
            return 2;
    }
}

public static GeneralEditDistance
getLevenshteinDistance(CharSequence pattern) {
    return new Levenshtein(pattern);
}

private GeneralEditDistances() {
}
}

class ModifiedBerghelRoachEditDistance implements GeneralEditDistance {

private static final int[] EMPTY_INT_ARRAY = new int[0];

public static ModifiedBerghelRoachEditDistance
getInstance(CharSequence pattern) {
    return getInstance(pattern.toString());
}

public static ModifiedBerghelRoachEditDistance
getInstance(String pattern) {
    return new ModifiedBerghelRoachEditDistance(pattern.toCharArray());
}

private int[] currentLeft = EMPTY_INT_ARRAY;

private int[] currentRight = EMPTY_INT_ARRAY;

private int[] lastLeft = EMPTY_INT_ARRAY;

private int[] lastRight = EMPTY_INT_ARRAY;

private final char[] pattern;

private int[] priorLeft = EMPTY_INT_ARRAY;

private int[] priorRight = EMPTY_INT_ARRAY;

private ModifiedBerghelRoachEditDistance(char[] pattern) {
    this.pattern = pattern;
}

public ModifiedBerghelRoachEditDistance duplicate() {
    return new ModifiedBerghelRoachEditDistance(pattern);
}

public int getDistance(CharSequence targetSequence, int limit) {
    final int targetLength = targetSequence.length();

    final int main = pattern.length - targetLength;
    int distance = Math.abs(main);
    if (distance > limit) {
        /* More than we wanted.  Give up right away */
        return Integer.MAX_VALUE;
    }

    final char[] target = new char[targetLength];
    for (int i = 0; i < targetLength; i++) {
        target[i] = targetSequence.charAt(i);
    }
    if (main <= 0) {
        ensureCapacityRight(distance, false);
        for (int j = 0; j <= distance; j++) {
            lastRight[j] = distance - j - 1;  /* Make diagonal -k start in row k */
            priorRight[j] = -1;
        }
    } else {
        ensureCapacityLeft(distance, false);
        for (int j = 0; j <= distance; j++) {
            lastLeft[j] = -1;                 /* Make diagonal +k start in row 0 */
            priorLeft[j] = -1;
        }
    }

    boolean even = true;

    while (true) {

        int offDiagonal = (distance - main) / 2;
        ensureCapacityRight(offDiagonal, true);

        if (even) {
            lastRight[offDiagonal] = -1;
        }

        int immediateRight = -1;
        for (; offDiagonal > 0; offDiagonal--) {
            currentRight[offDiagonal] = immediateRight = computeRow(
                    (main + offDiagonal),
                    (distance - offDiagonal),
                    pattern,
                    target,
                    priorRight[offDiagonal - 1],
                    lastRight[offDiagonal],
                    immediateRight);
        }

        offDiagonal = (distance + main) / 2;
        ensureCapacityLeft(offDiagonal, true);

        if (even) {
            lastLeft[offDiagonal] = (distance - main) / 2 - 1;
        }

        int immediateLeft = even ? -1 : (distance - main) / 2;

        for (; offDiagonal > 0; offDiagonal--) {
            currentLeft[offDiagonal] = immediateLeft = computeRow(
                    (main - offDiagonal),
                    (distance - offDiagonal),
                    pattern, target,
                    immediateLeft,
                    lastLeft[offDiagonal],
                    priorLeft[offDiagonal - 1]);
        }

        int mainRow = computeRow(main, distance, pattern, target,
                immediateLeft, lastLeft[0], immediateRight);

        if ((mainRow == targetLength) || (++distance > limit) || (distance < 0)) {
            break;
        }

        /* The [0] element goes to both sides. */
        currentLeft[0] = currentRight[0] = mainRow;

        /* Rotate rows around for next round: current=>last=>prior (=>current) */
        int[] tmp = priorLeft;
        priorLeft = lastLeft;
        lastLeft = currentLeft;
        currentLeft = priorLeft;

        tmp = priorRight;
        priorRight = lastRight;
        lastRight = currentRight;
        currentRight = tmp;

        /* Update evenness, too */
        even = !even;
    }

    return distance;
}

private int computeRow(int k, int p, char[] a, char[] b,
                       int knownLeft, int knownAbove, int knownRight) {
    assert (Math.abs(k) <= p);
    assert (p >= 0);

    int t;
    if (p == 0) {
        t = 0;
    } else {
        t = Math.max(Math.max(knownAbove, knownRight) + 1, knownLeft);
    }

    int tmax = Math.min(b.length, (a.length - k));

    while ((t < tmax) && b[t] == a[t + k]) {
        t++;
    }

    return t;
}

private void ensureCapacityLeft(int index, boolean copy) {
    if (currentLeft.length <= index) {
        index++;
        priorLeft = resize(priorLeft, index, copy);
        lastLeft = resize(lastLeft, index, copy);
        currentLeft = resize(currentLeft, index, false);
    }
}

private void ensureCapacityRight(int index, boolean copy) {
    if (currentRight.length <= index) {
        index++;
        priorRight = resize(priorRight, index, copy);
        lastRight = resize(lastRight, index, copy);
        currentRight = resize(currentRight, index, false);
    }
}

private int[] resize(int[] array, int size, boolean copy) {
    int[] result = new int[size];
    if (copy) {
        System.arraycopy(array, 0, result, 0, array.length);
    }
    return result;
}
}

abstract class MyersBitParallelEditDistance
    implements GeneralEditDistance, Cloneable {

static class Empty extends MyersBitParallelEditDistance {
    Empty(CharSequence s) {
        super(s);
    }

    @Override
    public GeneralEditDistance duplicate() {
        return this;      /* thread-safe */
    }

    @Override
    public int getDistance(CharSequence s, int k) {
        return s.length();
    }
}

static class Multi extends MyersBitParallelEditDistance {
    int count;
    final int lastBitPosition;
    final int[][] positions;
    int[] verticalNegativesReusable;
    int[] verticalPositivesReusable;
    final int wordMask = (-1 >>> 1);
    final int wordSize = Integer.SIZE - 1;

    Multi(CharSequence s) {
        super(s);
        count = (m + wordSize - 1) / wordSize;
        positions = PatternBitmap.map(s, idx, new int[idx.size()][], wordSize);
        lastBitPosition = (1 << ((m - 1) % wordSize));
        perThreadInit();
    }

    @Override
    public int getDistance(CharSequence s, int k) {
        indices = idx.map(s, indices);

        int[] verticalPositives = verticalPositivesReusable;
        java.util.Arrays.fill(verticalPositives, wordMask);
        int[] verticalNegatives = verticalNegativesReusable;
        java.util.Arrays.fill(verticalNegatives, 0);

        int distance = m;
        int len = s.length();

        int maxMisses = k + len - m;
        if (maxMisses < 0) {
            maxMisses = Integer.MAX_VALUE;
        }

        outer:
        for (int j = 0; j < len; j++) {
            int[] position = positions[indices[j]];

            int sum = 0;
            int horizontalPositiveShift = 1;
            int horizontalNegativeShift = 0;

            for (int i = 0; i < count; i++) {
                int verticalNegative = verticalNegatives[i];
                int patternMatch = (position[i] | verticalNegative);
                int verticalPositive = verticalPositives[i];
                sum = (verticalPositive & patternMatch)
                        + (verticalPositive) + (sum >>> wordSize);
                int diagonalZero = ((sum & wordMask) ^ verticalPositive)
                        | patternMatch;
                int horizontalPositive = (verticalNegative
                        | ~(diagonalZero | verticalPositive));
                int horizontalNegative = diagonalZero & verticalPositive;

                if (i == (count - 1)) {            /* only last bit in last word */
                    if ((horizontalNegative & lastBitPosition) != 0) {
                        distance--;
                    } else if ((horizontalPositive & lastBitPosition) != 0) {
                        distance++;
                        if ((maxMisses -= 2) < 0) {
                            break outer;
                        }
                    } else if (--maxMisses < 0) {
                        break outer;
                    }
                }

                horizontalPositive = ((horizontalPositive << 1)
                        | horizontalPositiveShift);
                horizontalPositiveShift = (horizontalPositive >>> wordSize);

                horizontalNegative = ((horizontalNegative << 1)
                        | horizontalNegativeShift);
                horizontalNegativeShift = (horizontalNegative >>> wordSize);

                verticalPositives[i] = (horizontalNegative
                        | ~(diagonalZero | horizontalPositive))
                        & wordMask;
                verticalNegatives[i] = (diagonalZero & horizontalPositive) & wordMask;
            }
        }
        return distance;
    }

    @Override
    protected void perThreadInit() {
        super.perThreadInit();
        verticalPositivesReusable = new int[count];
        verticalNegativesReusable = new int[count];
    }
}

static class TYPEint/*WORD*/ extends MyersBitParallelEditDistance {
    final int/*WORD*/ lastBitPosition;
    final int/*WORD*/[] map;

    @SuppressWarnings("cast")
    TYPEint/*WORD*/(CharSequence s) {
        super(s);
        /* Precompute bitmaps for this pattern */
        map = PatternBitmap.map(s, idx, new int/*WORD*/[idx.size()]);
        /* Compute the bit that represents a change in the last row */
        lastBitPosition = (((int/*WORD*/) 1) << (m - 1));
    }

    @Override
    public int getDistance(CharSequence s, int k) {
        int len = s.length();

        /* Quick check based on length */
        if (((len - m) > k) || ((m - len) > k)) {
            return k + 1;
        }

        /* Map characters to their integer positions in the bitmap array */
        indices = idx.map(s, indices);

        /* Initially, vertical change is all positive (none negative) */
        int/*WORD*/ verticalPositive = -1;
        int/*WORD*/ verticalNegative = 0;
        int distance = m;

        /* We can only miss the "distance--" below this many times: */
        int maxMisses = k + len - m;
        if (maxMisses < 0) {
            maxMisses = Integer.MAX_VALUE;
        }

        for (int j = 0; j < len; j++) {
            /* Where is diagonal zero: matches, or prior VN; plus recursion */
            int/*WORD*/ diagonalZero = map[indices[j]] | verticalNegative;
            diagonalZero |= (((diagonalZero & verticalPositive) + verticalPositive)
                    ^ verticalPositive);

            /* Compute horizontal changes */
            int/*WORD*/ horizontalPositive = verticalNegative
                    | ~(diagonalZero | verticalPositive);
            int/*WORD*/ horizontalNegative = diagonalZero & verticalPositive;

            /* Update final distance based on horizontal changes */
            if ((horizontalNegative & lastBitPosition) != 0) {
                distance--;
            } else if ((horizontalPositive & lastBitPosition) != 0) {
                distance++;
                if ((maxMisses -= 2) < 0) {
                    break;
                }
            } else if (--maxMisses < 0) {
                break;
            }

            /* Shift Hs to next row, compute new Vs analagously to Hs above */
            horizontalPositive = (horizontalPositive << 1) | 1;
            verticalPositive = (horizontalNegative << 1)
                    | ~(diagonalZero | horizontalPositive);
            verticalNegative = diagonalZero & horizontalPositive;
        }
        return distance;
    }
}

static class TYPElong/*WORD*/ extends MyersBitParallelEditDistance {
    final long/*WORD*/ lastBitPosition;
    final long/*WORD*/[] map;

    TYPElong/*WORD*/(CharSequence s) {
        super(s);
        /* Precompute bitmaps for this pattern */
        map = PatternBitmap.map(s, idx, new long/*WORD*/[idx.size()]);
        /* Compute the bit that represents a change in the last row */
        lastBitPosition = (((long/*WORD*/) 1) << (m - 1));
    }

    @Override
    public int getDistance(CharSequence s, int k) {
        int len = s.length();

        /* Quick check based on length */
        if (((len - m) > k) || ((m - len) > k)) {
            return k + 1;
        }

        /* Map characters to their integer positions in the bitmap array */
        indices = idx.map(s, indices);

        /* Initially, vertical change is all positive (none negative) */
        long/*WORD*/ verticalPositive = -1;
        long/*WORD*/ verticalNegative = 0;
        int distance = m;

        /* We can only miss the "distance--" below this many times: */
        int maxMisses = k + len - m;
        if (maxMisses < 0) {
            maxMisses = Integer.MAX_VALUE;
        }

        for (int j = 0; j < len; j++) {
            /* Where is diagonal zero: matches, or prior VN; plus recursion */
            long/*WORD*/ diagonalZero = map[indices[j]] | verticalNegative;
            diagonalZero |= (((diagonalZero & verticalPositive) + verticalPositive)
                    ^ verticalPositive);

            /* Compute horizontal changes */
            long/*WORD*/ horizontalPositive = verticalNegative
                    | ~(diagonalZero | verticalPositive);
            long/*WORD*/ horizontalNegative = diagonalZero & verticalPositive;

            /* Update final distance based on horizontal changes */
            if ((horizontalNegative & lastBitPosition) != 0) {
                distance--;
            } else if ((horizontalPositive & lastBitPosition) != 0) {
                distance++;
                if ((maxMisses -= 2) < 0) {
                    break;
                }
            } else if (--maxMisses < 0) {
                break;
            }

            /* Shift Hs to next row, compute new Vs analagously to Hs above */
            horizontalPositive = (horizontalPositive << 1) | 1;
            verticalPositive = (horizontalNegative << 1)
                    | ~(diagonalZero | horizontalPositive);
            verticalNegative = diagonalZero & horizontalPositive;
        }
        return distance;
    }
}

public static MyersBitParallelEditDistance getInstance(CharSequence s) {
    int m = s.length();
    return (m <= Integer.SIZE) ?
            ((m == 0) ? new Empty(s) : new TYPEint(s)) :
            (s.length() <= Long.SIZE) ?
                    new TYPElong(s) :
                    new Multi(s);
}

final CharIndex idx;

int[] indices = new int[0];

final int m;

protected MyersBitParallelEditDistance(CharSequence s) {
    m = s.length();
    idx = CharIndex.getInstance(s);
}

public GeneralEditDistance duplicate() {
    try {
        return (MyersBitParallelEditDistance) clone();
    } catch (CloneNotSupportedException x) { /*IMPOSSIBLE */
        throw new IllegalStateException("Cloneable object would not clone");
    }
}

public abstract int getDistance(CharSequence s, int k);

@Override
protected Object clone() throws CloneNotSupportedException {
    Object obj = super.clone();

    /* Re-initialize any non-thread-safe parts */
    ((MyersBitParallelEditDistance) obj).perThreadInit();

    return obj;
}

protected void perThreadInit() {
    indices = new int[0];
}
}

class PatternBitmap {

public static int[] map(CharSequence s, CharIndex idx, int[] result) {
    int len = s.length();
    assert (len <= Integer.SIZE);
    for (int i = 0; i < len; i++) {
        result[idx.lookup(s.charAt(i))] |= (1 << i);
    }
    return result;
}

public static int[][] map(CharSequence s, CharIndex idx,
                          int[][] result, int width) {
    assert (width <= Integer.SIZE);
    int len = s.length();
    int rowSize = (len + width - 1) / width;

    /*
    * Use one zero-filled bitmap for alphabet characters not in the pattern
    */
    int[] nullElement = new int[rowSize];
    java.util.Arrays.fill(result, nullElement);

    int wordIndex = 0;          /* Which word we are on now */
    int bitWithinWord = 0;      /* Which bit within that word */

    for (int i = 0; i < s.length(); i++) {
        int[] r = result[idx.lookup(s.charAt(i))];
        if (r == nullElement) {

            /* Create a separate zero-filled bitmap for this alphabet character */
            r = result[idx.lookup(s.charAt(i))] = new int[rowSize];
        }
        r[wordIndex] |= (1 << bitWithinWord);

        /* Step to the next bit (and word if appropriate) */
        if (++bitWithinWord == width) {
            bitWithinWord = 0;
            wordIndex++;
        }
    }
    return result;
}

public static long[] map(CharSequence s, CharIndex idx, long[] result) {
    int len = s.length();
    assert (len <= Long.SIZE);
    for (int i = 0; i < len; i++) {
        result[idx.lookup(s.charAt(i))] |= (1L << i);
    }
    return result;
}

private PatternBitmap() { /* Prevent instantiation */ }
}
\$\endgroup\$
  • \$\begingroup\$ +1 for all that work. Haha, I ended up going a totally different route, but if I ever do this kind of thing again I imagine your code will be helpful (and will hopefully be helpful to someone in the future). I hope it was helpful for you too. \$\endgroup\$ – kentcdodds May 31 '12 at 13:09
  • \$\begingroup\$ Thanks. There are more interesting structures (trie) for comparing levenstein distance between few hundreds strings in milliseconds: stevehanov.ca/blog/index.php?id=114 \$\endgroup\$ – cat_baxter May 31 '12 at 13:33

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