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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 and up.
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package org.bouncycastle.crypto.generators;

import org.bouncycastle.crypto.CipherKeyGenerator;
import org.bouncycastle.crypto.KeyGenerationParameters;
import org.bouncycastle.crypto.macs.Poly1305;

/**
 * Generates keys for the Poly1305 MAC.
 * 
 * Poly1305 keys are 256 bit keys consisting of a 128 bit secret key used for the underlying block
 * cipher followed by a 128 bit {@code r} value used for the polynomial portion of the Mac. 

 * The {@code r} value has a specific format with some bits required to be cleared, resulting in an
 * effective 106 bit key. 

 * A separately generated 256 bit key can be modified to fit the Poly1305 key format by using the
 * {@link #clamp(byte[])} method to clear the required bits.
 *
 * @see Poly1305
 */
public class Poly1305KeyGenerator
    extends CipherKeyGenerator
{
    private static final byte R_MASK_LOW_2 = (byte)0xFC;
    private static final byte R_MASK_HIGH_4 = (byte)0x0F;

    /**
     * Initialises the key generator.

     * Poly1305 keys are always 256 bits, so the key length in the provided parameters is ignored.
     */
    public void init(KeyGenerationParameters param)
    {
        // Poly1305 keys are always 256 bits
        super.init(new KeyGenerationParameters(param.getRandom(), 256));
    }

    /**
     * Generates a 256 bit key in the format required for Poly1305 - e.g.
     * k[0] ... k[15], r[0] ... r[15] with the required bits in r cleared
     * as per {@link #clamp(byte[])}.
     */
    public byte[] generateKey()
    {
        final byte[] key = super.generateKey();
        clamp(key);
        return key;
    }

    /**
     * Modifies an existing 32 byte key value to comply with the requirements of the Poly1305 key by
     * clearing required bits in the r (second 16 bytes) portion of the key.

     * Specifically:
     * 

     * r[3], r[7], r[11], r[15] have top four bits clear (i.e., are {0, 1, . . . , 15})
     * r[4], r[8], r[12] have bottom two bits clear (i.e., are in {0, 4, 8, . . . , 252})
     * 
     *
     * @param key a 32 byte key value k[0] ... k[15], r[0] ... r[15]
     */
    public static void clamp(byte[] key)
    {
        /*
         * Key is k[0] ... k[15], r[0] ... r[15] as per poly1305_aes_clamp in ref impl.
         */
        if (key.length != 32)
        {
            throw new IllegalArgumentException("Poly1305 key must be 256 bits.");
        }

        /*
         * r[3], r[7], r[11], r[15] have top four bits clear (i.e., are {0, 1, . . . , 15})
         */
        key[3] &= R_MASK_HIGH_4;
        key[7] &= R_MASK_HIGH_4;
        key[11] &= R_MASK_HIGH_4;
        key[15] &= R_MASK_HIGH_4;

        /*
         * r[4], r[8], r[12] have bottom two bits clear (i.e., are in {0, 4, 8, . . . , 252}).
         */
        key[4] &= R_MASK_LOW_2;
        key[8] &= R_MASK_LOW_2;
        key[12] &= R_MASK_LOW_2;
    }

    /**
     * Checks a 32 byte key for compliance with the Poly1305 key requirements, e.g.
     * k[0] ... k[15], r[0] ... r[15] with the required bits in r cleared
     * as per {@link #clamp(byte[])}.
     *
     * @throws IllegalArgumentException if the key is of the wrong length, or has invalid bits set
     *             in the r portion of the key.
     */
    public static void checkKey(byte[] key)
    {
        if (key.length != 32)
        {
            throw new IllegalArgumentException("Poly1305 key must be 256 bits.");
        }

        checkMask(key[3], R_MASK_HIGH_4);
        checkMask(key[7], R_MASK_HIGH_4);
        checkMask(key[11], R_MASK_HIGH_4);
        checkMask(key[15], R_MASK_HIGH_4);

        checkMask(key[4], R_MASK_LOW_2);
        checkMask(key[8], R_MASK_LOW_2);
        checkMask(key[12], R_MASK_LOW_2);
    }

    private static void checkMask(byte b, byte mask)
    {
        if ((b & (~mask)) != 0)
        {
            throw new IllegalArgumentException("Invalid format for r portion of Poly1305 key.");
        }
    }

}