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The Bouncy Castle Java APIs for CMS, PKCS, EAC, TSP, CMP, CRMF, OCSP, and certificate generation. This jar contains APIs for JDK 1.4. The APIs can be used in conjunction with a JCE/JCA provider such as the one provided with the Bouncy Castle Cryptography APIs.
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package org.bouncycastle.tsp.ers;

import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Comparator;
import java.util.Iterator;
import java.util.List;

import org.bouncycastle.asn1.tsp.PartialHashtree;
import org.bouncycastle.operator.DigestCalculator;
import org.bouncycastle.util.io.Streams;

class ERSUtil
{
    private ERSUtil()
    {

    }

    private static final Comparator  hashComp = new ByteArrayComparator();

    static byte[] calculateDigest(DigestCalculator digCalc, byte[] data)
    {
        try
        {
            OutputStream mdOut = digCalc.getOutputStream();

            mdOut.write(data);

            mdOut.close();

            return digCalc.getDigest();
        }
        catch (IOException e)
        {
            throw ExpUtil.createIllegalState("unable to calculate hash: " + e.getMessage(), e);
        }
    }

    static byte[] calculateBranchHash(DigestCalculator digCalc, byte[] a, byte[] b)
    {
        if (hashComp.compare(a, b) <= 0)
        {
            return calculateDigest(digCalc, a, b);
        }
        else
        {
            return calculateDigest(digCalc, b, a);
        }
    }

    static byte[] calculateBranchHash(DigestCalculator digCalc, byte[][] values)
    {
        if (values.length == 2)
        {
            return calculateBranchHash(digCalc, values[0], values[1]);
        }

        return calculateDigest(digCalc, buildIndexedHashList(values).iterator());
    }

    static byte[] calculateDigest(DigestCalculator digCalc, byte[] a, byte[] b)
    {
        try
        {
            OutputStream mdOut = digCalc.getOutputStream();

            mdOut.write(a);
            mdOut.write(b);

            mdOut.close();

            return digCalc.getDigest();
        }
        catch (IOException e)
        {
            throw ExpUtil.createIllegalState("unable to calculate hash: " + e.getMessage(), e);
        }
    }

    static byte[] calculateDigest(DigestCalculator digCalc, Iterator  dataGroup)
    {
        try
        {
            OutputStream mdOut = digCalc.getOutputStream();
            while (dataGroup.hasNext())
            {
                mdOut.write((byte[])dataGroup.next());
            }

            mdOut.close();

            return digCalc.getDigest();
        }
        catch (IOException e)
        {
            throw ExpUtil.createIllegalState("unable to calculate hash: " + e.getMessage(), e);
        }
    }

    static byte[] calculateDigest(DigestCalculator digCalc, InputStream inStream)
    {
        try
        {
            OutputStream mdOut = digCalc.getOutputStream();

            Streams.pipeAll(inStream, mdOut);

            mdOut.close();

            return digCalc.getDigest();
        }
        catch (IOException e)
        {
            throw ExpUtil.createIllegalState("unable to calculate hash: " + e.getMessage(), e);
        }
    }

    static byte[] computeNodeHash(DigestCalculator digCalc, PartialHashtree node)
    {
        byte[][] values = node.getValues();

        if (values.length > 1)
        {
            return calculateDigest(digCalc, buildIndexedHashList(values).iterator());
        }

        return values[0];
    }

    static List  buildIndexedHashList(byte[][] values)
    {
        SortedHashList hashes = new SortedHashList();

        for (int i = 0; i != values.length; i++)
        {
            hashes.add(values[i]);
        }

        return hashes.toList();
    }

    static List  buildHashList(DigestCalculator digCalc, List  dataObjects, byte[] previousChainHash)
    {
        SortedHashList hashes = new SortedHashList();

        for (int i = 0; i != dataObjects.size(); i++)
        {
            hashes.add(((ERSData)dataObjects.get(i)).getHash(digCalc, previousChainHash));
        }

        return hashes.toList();
    }

    static List  buildIndexedHashList(DigestCalculator digCalc, List  dataObjects, byte[] previousChainsHash)
    {
        SortedIndexedHashList hashes = new SortedIndexedHashList();

        for (int i = 0; i != dataObjects.size(); i++)
        {
            byte[] hash = ((ERSData)dataObjects.get(i)).getHash(digCalc, previousChainsHash);

            hashes.add(new IndexedHash(i, hash));
        }

        return hashes.toList();
    }

    static byte[] concatPreviousHashes(DigestCalculator digCalc, byte[] chainHash, byte[] dataHash)
    {
        if (chainHash == null)
        {
            return dataHash;
        }

        try
        {
            OutputStream digOut = digCalc.getOutputStream();

            digOut.write(dataHash);
            digOut.write(chainHash);
            digOut.close();

            return digCalc.getDigest();
        }
        catch (IOException e)
        {
            // should never happen
            throw new IllegalStateException("unable to hash data");
        }
    }
}