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The Bouncy Castle Crypto package is a Java implementation of cryptographic algorithms. This jar contains JCE provider and lightweight API for the Bouncy Castle Cryptography APIs for JDK 1.5 to JDK 1.8.
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package org.bouncycastle.crypto.digests;

import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Vector;

import org.bouncycastle.crypto.OutputLengthException;
import org.bouncycastle.crypto.engines.ThreefishEngine;
import org.bouncycastle.crypto.macs.SkeinMac;
import org.bouncycastle.crypto.params.SkeinParameters;
import org.bouncycastle.util.Arrays;
import org.bouncycastle.util.Integers;
import org.bouncycastle.util.Memoable;

/**
 * Implementation of the Skein family of parameterised hash functions in 256, 512 and 1024 bit block
 * sizes, based on the {@link ThreefishEngine Threefish} tweakable block cipher.
 * 
 * This is the 1.3 version of Skein defined in the Skein hash function submission to the NIST SHA-3
 * competition in October 2010.
 * 

 * Skein was designed by Niels Ferguson - Stefan Lucks - Bruce Schneier - Doug Whiting - Mihir
 * Bellare - Tadayoshi Kohno - Jon Callas - Jesse Walker.
 * 

 * This implementation is the basis for {@link SkeinDigest} and {@link SkeinMac}, implementing the
 * parameter based configuration system that allows Skein to be adapted to multiple applications. 

 * Initialising the engine with {@link SkeinParameters} allows standard and arbitrary parameters to
 * be applied during the Skein hash function.
 * 

 * Implemented:
 * 

 * 256, 512 and 1024 bit internal states.
 * Full 96 bit input length.
 * Parameters defined in the Skein specification, and arbitrary other pre and post message
 * parameters.
 * Arbitrary output size in 1 byte intervals.
 * 
 * 
 * Not implemented:
 * 

 * Sub-byte length input (bit padding).
 * Tree hashing.
 * 
 *
 * @see SkeinParameters
 */
public class SkeinEngine
    implements Memoable
{
    /**
     * 256 bit block size - Skein 256
     */
    public static final int SKEIN_256 = ThreefishEngine.BLOCKSIZE_256;
    /**
     * 512 bit block size - Skein 512
     */
    public static final int SKEIN_512 = ThreefishEngine.BLOCKSIZE_512;
    /**
     * 1024 bit block size - Skein 1024
     */
    public static final int SKEIN_1024 = ThreefishEngine.BLOCKSIZE_1024;

    // Minimal at present, but more complex when tree hashing is implemented
    private static class Configuration
    {
        private byte[] bytes = new byte[32];

        public Configuration(long outputSizeBits)
        {
            // 0..3 = ASCII SHA3
            bytes[0] = (byte)'S';
            bytes[1] = (byte)'H';
            bytes[2] = (byte)'A';
            bytes[3] = (byte)'3';

            // 4..5 = version number in LSB order
            bytes[4] = 1;
            bytes[5] = 0;

            // 8..15 = output length
            ThreefishEngine.wordToBytes(outputSizeBits, bytes, 8);
        }

        public byte[] getBytes()
        {
            return bytes;
        }

    }

    public static class Parameter
    {
        private int type;
        private byte[] value;

        public Parameter(int type, byte[] value)
        {
            this.type = type;
            this.value = value;
        }

        public int getType()
        {
            return type;
        }

        public byte[] getValue()
        {
            return value;
        }

    }

    /**
     * The parameter type for the Skein key.
     */
    private static final int PARAM_TYPE_KEY = 0;

    /**
     * The parameter type for the Skein configuration block.
     */
    private static final int PARAM_TYPE_CONFIG = 4;

    /**
     * The parameter type for the message.
     */
    private static final int PARAM_TYPE_MESSAGE = 48;

    /**
     * The parameter type for the output transformation.
     */
    private static final int PARAM_TYPE_OUTPUT = 63;

    /**
     * Precalculated UBI(CFG) states for common state/output combinations without key or other
     * pre-message params.
     */
    private static final Hashtable INITIAL_STATES = new Hashtable();

    static
    {
        // From Appendix C of the Skein 1.3 NIST submission
        initialState(SKEIN_256, 128, new long[]{
            0xe1111906964d7260L,
            0x883daaa77c8d811cL,
            0x10080df491960f7aL,
            0xccf7dde5b45bc1c2L});

        initialState(SKEIN_256, 160, new long[]{
            0x1420231472825e98L,
            0x2ac4e9a25a77e590L,
            0xd47a58568838d63eL,
            0x2dd2e4968586ab7dL});

        initialState(SKEIN_256, 224, new long[]{
            0xc6098a8c9ae5ea0bL,
            0x876d568608c5191cL,
            0x99cb88d7d7f53884L,
            0x384bddb1aeddb5deL});

        initialState(SKEIN_256, 256, new long[]{
            0xfc9da860d048b449L,
            0x2fca66479fa7d833L,
            0xb33bc3896656840fL,
            0x6a54e920fde8da69L});

        initialState(SKEIN_512, 128, new long[]{
            0xa8bc7bf36fbf9f52L,
            0x1e9872cebd1af0aaL,
            0x309b1790b32190d3L,
            0xbcfbb8543f94805cL,
            0x0da61bcd6e31b11bL,
            0x1a18ebead46a32e3L,
            0xa2cc5b18ce84aa82L,
            0x6982ab289d46982dL});

        initialState(SKEIN_512, 160, new long[]{
            0x28b81a2ae013bd91L,
            0xc2f11668b5bdf78fL,
            0x1760d8f3f6a56f12L,
            0x4fb747588239904fL,
            0x21ede07f7eaf5056L,
            0xd908922e63ed70b8L,
            0xb8ec76ffeccb52faL,
            0x01a47bb8a3f27a6eL});

        initialState(SKEIN_512, 224, new long[]{
            0xccd0616248677224L,
            0xcba65cf3a92339efL,
            0x8ccd69d652ff4b64L,
            0x398aed7b3ab890b4L,
            0x0f59d1b1457d2bd0L,
            0x6776fe6575d4eb3dL,
            0x99fbc70e997413e9L,
            0x9e2cfccfe1c41ef7L});

        initialState(SKEIN_512, 384, new long[]{
            0xa3f6c6bf3a75ef5fL,
            0xb0fef9ccfd84faa4L,
            0x9d77dd663d770cfeL,
            0xd798cbf3b468fddaL,
            0x1bc4a6668a0e4465L,
            0x7ed7d434e5807407L,
            0x548fc1acd4ec44d6L,
            0x266e17546aa18ff8L});

        initialState(SKEIN_512, 512, new long[]{
            0x4903adff749c51ceL,
            0x0d95de399746df03L,
            0x8fd1934127c79bceL,
            0x9a255629ff352cb1L,
            0x5db62599df6ca7b0L,
            0xeabe394ca9d5c3f4L,
            0x991112c71a75b523L,
            0xae18a40b660fcc33L});
    }

    private static void initialState(int blockSize, int outputSize, long[] state)
    {
        INITIAL_STATES.put(variantIdentifier(blockSize / 8, outputSize / 8), state);
    }

    private static Integer variantIdentifier(int blockSizeBytes, int outputSizeBytes)
    {
        return Integers.valueOf((outputSizeBytes << 16) | blockSizeBytes);
    }

    private static class UbiTweak
    {
        /**
         * Point at which position might overflow long, so switch to add with carry logic
         */
        private static final long LOW_RANGE = Long.MAX_VALUE - Integer.MAX_VALUE;

        /**
         * Bit 127 = final
         */
        private static final long T1_FINAL = 1L << 63;

        /**
         * Bit 126 = first
         */
        private static final long T1_FIRST = 1L << 62;

        /**
         * UBI uses a 128 bit tweak
         */
        private long tweak[] = new long[2];

        /**
         * Whether 64 bit position exceeded
         */
        private boolean extendedPosition;

        public UbiTweak()
        {
            reset();
        }

        public void reset(UbiTweak tweak)
        {
            this.tweak = Arrays.clone(tweak.tweak, this.tweak);
            this.extendedPosition = tweak.extendedPosition;
        }

        public void reset()
        {
            tweak[0] = 0;
            tweak[1] = 0;
            extendedPosition = false;
            setFirst(true);
        }

        public void setType(int type)
        {
            // Bits 120..125 = type
            tweak[1] = (tweak[1] & 0xFFFFFFC000000000L) | ((type & 0x3FL) << 56);
        }

        public int getType()
        {
            return (int)((tweak[1] >>> 56) & 0x3FL);
        }

        public void setFirst(boolean first)
        {
            if (first)
            {
                tweak[1] |= T1_FIRST;
            }
            else
            {
                tweak[1] &= ~T1_FIRST;
            }
        }

        public boolean isFirst()
        {
            return ((tweak[1] & T1_FIRST) != 0);
        }

        public void setFinal(boolean last)
        {
            if (last)
            {
                tweak[1] |= T1_FINAL;
            }
            else
            {
                tweak[1] &= ~T1_FINAL;
            }
        }

        public boolean isFinal()
        {
            return ((tweak[1] & T1_FINAL) != 0);
        }

        /**
         * Advances the position in the tweak by the specified value.
         */
        public void advancePosition(int advance)
        {
            // Bits 0..95 = position
            if (extendedPosition)
            {
                long[] parts = new long[3];
                parts[0] = tweak[0] & 0xFFFFFFFFL;
                parts[1] = (tweak[0] >>> 32) & 0xFFFFFFFFL;
                parts[2] = tweak[1] & 0xFFFFFFFFL;

                long carry = advance;
                for (int i = 0; i < parts.length; i++)
                {
                    carry += parts[i];
                    parts[i] = carry;
                    carry >>>= 32;
                }
                tweak[0] = ((parts[1] & 0xFFFFFFFFL) << 32) | (parts[0] & 0xFFFFFFFFL);
                tweak[1] = (tweak[1] & 0xFFFFFFFF00000000L) | (parts[2] & 0xFFFFFFFFL);
            }
            else
            {
                long position = tweak[0];
                position += advance;
                tweak[0] = position;
                if (position > LOW_RANGE)
                {
                    extendedPosition = true;
                }
            }
        }

        public long[] getWords()
        {
            return tweak;
        }

        public String toString()
        {
            return getType() + " first: " + isFirst() + ", final: " + isFinal();
        }

    }

    /**
     * The Unique Block Iteration chaining mode.
     */
    // TODO: This might be better as methods...
    private class UBI
    {
        private final UbiTweak tweak = new UbiTweak();

        /**
         * Buffer for the current block of message data
         */
        private byte[] currentBlock;

        /**
         * Offset into the current message block
         */
        private int currentOffset;

        /**
         * Buffer for message words for feedback into encrypted block
         */
        private long[] message;

        public UBI(int blockSize)
        {
            currentBlock = new byte[blockSize];
            message = new long[currentBlock.length / 8];
        }

        public void reset(UBI ubi)
        {
            currentBlock = Arrays.clone(ubi.currentBlock, currentBlock);
            currentOffset = ubi.currentOffset;
            message = Arrays.clone(ubi.message, this.message);
            tweak.reset(ubi.tweak);
        }

        public void reset(int type)
        {
            tweak.reset();
            tweak.setType(type);
            currentOffset = 0;
        }

        public void update(byte[] value, int offset, int len, long[] output)
        {
            /*
             * Buffer complete blocks for the underlying Threefish cipher, only flushing when there
             * are subsequent bytes (last block must be processed in doFinal() with final=true set).
             */
            int copied = 0;
            while (len > copied)
            {
                if (currentOffset == currentBlock.length)
                {
                    processBlock(output);
                    tweak.setFirst(false);
                    currentOffset = 0;
                }

                int toCopy = Math.min((len - copied), currentBlock.length - currentOffset);
                System.arraycopy(value, offset + copied, currentBlock, currentOffset, toCopy);
                copied += toCopy;
                currentOffset += toCopy;
                tweak.advancePosition(toCopy);
            }
        }

        private void processBlock(long[] output)
        {
            threefish.init(true, chain, tweak.getWords());
            for (int i = 0; i < message.length; i++)
            {
                message[i] = ThreefishEngine.bytesToWord(currentBlock, i * 8);
            }

            threefish.processBlock(message, output);

            for (int i = 0; i < output.length; i++)
            {
                output[i] ^= message[i];
            }
        }

        public void doFinal(long[] output)
        {
            // Pad remainder of current block with zeroes
            for (int i = currentOffset; i < currentBlock.length; i++)
            {
                currentBlock[i] = 0;
            }

            tweak.setFinal(true);
            processBlock(output);
        }

    }

    /**
     * Underlying Threefish tweakable block cipher
     */
    final ThreefishEngine threefish;

    /**
     * Size of the digest output, in bytes
     */
    private final int outputSizeBytes;

    /**
     * The current chaining/state value
     */
    long[] chain;

    /**
     * The initial state value
     */
    private long[] initialState;

    /**
     * The (optional) key parameter
     */
    private byte[] key;

    /**
     * Parameters to apply prior to the message
     */
    private Parameter[] preMessageParameters;

    /**
     * Parameters to apply after the message, but prior to output
     */
    private Parameter[] postMessageParameters;

    /**
     * The current UBI operation
     */
    private final UBI ubi;

    /**
     * Buffer for single byte update method
     */
    private final byte[] singleByte = new byte[1];

    /**
     * Constructs a Skein engine.
     *
     * @param blockSizeBits  the internal state size in bits - one of {@link #SKEIN_256}, {@link #SKEIN_512} or
     *                       {@link #SKEIN_1024}.
     * @param outputSizeBits the output/digest size to produce in bits, which must be an integral number of
     *                       bytes.
     */
    public SkeinEngine(int blockSizeBits, int outputSizeBits)
    {
        if (outputSizeBits % 8 != 0)
        {
            throw new IllegalArgumentException("Output size must be a multiple of 8 bits. :" + outputSizeBits);
        }
        // TODO: Prevent digest sizes > block size?
        this.outputSizeBytes = outputSizeBits / 8;

        this.threefish = new ThreefishEngine(blockSizeBits);
        this.ubi = new UBI(threefish.getBlockSize());
    }

    /**
     * Creates a SkeinEngine as an exact copy of an existing instance.
     */
    public SkeinEngine(SkeinEngine engine)
    {
        this(engine.getBlockSize() * 8, engine.getOutputSize() * 8);
        copyIn(engine);
    }

    private void copyIn(SkeinEngine engine)
    {
        this.ubi.reset(engine.ubi);
        this.chain = Arrays.clone(engine.chain, this.chain);
        this.initialState = Arrays.clone(engine.initialState, this.initialState);
        this.key = Arrays.clone(engine.key, this.key);
        this.preMessageParameters = clone(engine.preMessageParameters, this.preMessageParameters);
        this.postMessageParameters = clone(engine.postMessageParameters, this.postMessageParameters);
    }

    private static Parameter[] clone(Parameter[] data, Parameter[] existing)
    {
        if (data == null)
        {
            return null;
        }
        if ((existing == null) || (existing.length != data.length))
        {
            existing = new Parameter[data.length];
        }
        System.arraycopy(data, 0, existing, 0, existing.length);
        return existing;
    }

    public Memoable copy()
    {
        return new SkeinEngine(this);
    }

    public void reset(Memoable other)
    {
        SkeinEngine s = (SkeinEngine)other;
        if ((getBlockSize() != s.getBlockSize()) || (outputSizeBytes != s.outputSizeBytes))
        {
            throw new IllegalArgumentException("Incompatible parameters in provided SkeinEngine.");
        }
        copyIn(s);
    }

    public int getOutputSize()
    {
        return outputSizeBytes;
    }

    public int getBlockSize()
    {
        return threefish.getBlockSize();
    }

    /**
     * Initialises the Skein engine with the provided parameters. See {@link SkeinParameters} for
     * details on the parameterisation of the Skein hash function.
     *
     * @param params the parameters to apply to this engine, or null to use no parameters.
     */
    public void init(SkeinParameters params)
    {
        this.chain = null;
        this.key = null;
        this.preMessageParameters = null;
        this.postMessageParameters = null;

        if (params != null)
        {
            byte[] key = params.getKey();
            if (key.length < 16)
            {
                throw new IllegalArgumentException("Skein key must be at least 128 bits.");
            }
            initParams(params.getParameters());
        }
        createInitialState();

        // Initialise message block
        ubiInit(PARAM_TYPE_MESSAGE);
    }

    private void initParams(Hashtable parameters)
    {
        Enumeration keys = parameters.keys();
        final Vector pre = new Vector();
        final Vector post = new Vector();

        while (keys.hasMoreElements())
        {
            Integer type = (Integer)keys.nextElement();
            byte[] value = (byte[])parameters.get(type);

            if (type.intValue() == PARAM_TYPE_KEY)
            {
                this.key = value;
            }
            else if (type.intValue() < PARAM_TYPE_MESSAGE)
            {
                pre.addElement(new Parameter(type.intValue(), value));
            }
            else
            {
                post.addElement(new Parameter(type.intValue(), value));
            }
        }
        preMessageParameters = new Parameter[pre.size()];
        pre.copyInto(preMessageParameters);
        sort(preMessageParameters);

        postMessageParameters = new Parameter[post.size()];
        post.copyInto(postMessageParameters);
        sort(postMessageParameters);
    }

    private static void sort(Parameter[] params)
    {
        if (params == null)
        {
            return;
        }
        // Insertion sort, for Java 1.1 compatibility
        for (int i = 1; i < params.length; i++)
        {
            Parameter param = params[i];
            int hole = i;
            while (hole > 0 && param.getType() < params[hole - 1].getType())
            {
                params[hole] = params[hole - 1];
                hole = hole - 1;
            }
            params[hole] = param;
        }
    }

    /**
     * Calculate the initial (pre message block) chaining state.
     */
    private void createInitialState()
    {
        long[] precalc = (long[])INITIAL_STATES.get(variantIdentifier(getBlockSize(), getOutputSize()));
        if ((key == null) && (precalc != null))
        {
            // Precalculated UBI(CFG)
            chain = Arrays.clone(precalc);
        }
        else
        {
            // Blank initial state
            chain = new long[getBlockSize() / 8];

            // Process key block
            if (key != null)
            {
                ubiComplete(SkeinParameters.PARAM_TYPE_KEY, key);
            }

            // Process configuration block
            ubiComplete(PARAM_TYPE_CONFIG, new Configuration(outputSizeBytes * 8).getBytes());
        }

        // Process additional pre-message parameters
        if (preMessageParameters != null)
        {
            for (int i = 0; i < preMessageParameters.length; i++)
            {
                Parameter param = preMessageParameters[i];
                ubiComplete(param.getType(), param.getValue());
            }
        }
        initialState = Arrays.clone(chain);
    }

    /**
     * Reset the engine to the initial state (with the key and any pre-message parameters , ready to
     * accept message input.
     */
    public void reset()
    {
        System.arraycopy(initialState, 0, chain, 0, chain.length);

        ubiInit(PARAM_TYPE_MESSAGE);
    }

    private void ubiComplete(int type, byte[] value)
    {
        ubiInit(type);
        this.ubi.update(value, 0, value.length, chain);
        ubiFinal();
    }

    private void ubiInit(int type)
    {
        this.ubi.reset(type);
    }

    private void ubiFinal()
    {
        ubi.doFinal(chain);
    }

    private void checkInitialised()
    {
        if (this.ubi == null)
        {
            throw new IllegalArgumentException("Skein engine is not initialised.");
        }
    }

    public void update(byte in)
    {
        singleByte[0] = in;
        update(singleByte, 0, 1);
    }

    public void update(byte[] in, int inOff, int len)
    {
        checkInitialised();
        ubi.update(in, inOff, len, chain);
    }

    public int doFinal(byte[] out, int outOff)
    {
        checkInitialised();
        if (out.length < (outOff + outputSizeBytes))
        {
            throw new OutputLengthException("Output buffer is too short to hold output");
        }

        // Finalise message block
        ubiFinal();

        // Process additional post-message parameters
        if (postMessageParameters != null)
        {
            for (int i = 0; i < postMessageParameters.length; i++)
            {
                Parameter param = postMessageParameters[i];
                ubiComplete(param.getType(), param.getValue());
            }
        }

        // Perform the output transform
        final int blockSize = getBlockSize();
        final int blocksRequired = ((outputSizeBytes + blockSize - 1) / blockSize);
        for (int i = 0; i < blocksRequired; i++)
        {
            final int toWrite = Math.min(blockSize, outputSizeBytes - (i * blockSize));
            output(i, out, outOff + (i * blockSize), toWrite);
        }

        reset();

        return outputSizeBytes;
    }

    private void output(long outputSequence, byte[] out, int outOff, int outputBytes)
    {
        byte[] currentBytes = new byte[8];
        ThreefishEngine.wordToBytes(outputSequence, currentBytes, 0);

        // Output is a sequence of UBI invocations all of which use and preserve the pre-output
        // state
        long[] outputWords = new long[chain.length];
        ubiInit(PARAM_TYPE_OUTPUT);
        this.ubi.update(currentBytes, 0, currentBytes.length, outputWords);
        ubi.doFinal(outputWords);

        final int wordsRequired = ((outputBytes + 8 - 1) / 8);
        for (int i = 0; i < wordsRequired; i++)
        {
            int toWrite = Math.min(8, outputBytes - (i * 8));
            if (toWrite == 8)
            {
                ThreefishEngine.wordToBytes(outputWords[i], out, outOff + (i * 8));
            }
            else
            {
                ThreefishEngine.wordToBytes(outputWords[i], currentBytes, 0);
                System.arraycopy(currentBytes, 0, out, outOff + (i * 8), toWrite);
            }
        }
    }

}