CSG_MD5.h

//
// This is a C++ friendly, limited use MD5 checksum copied
// from the reference implementation at http://www.ietf.org/rfc/rfc1321.txt
//
// The sole purpose of this file is to eliminate dependence on the
// openssl MD5 code, which poses a maintenance problem for general
// users trying to build libstatgen.
//
// It is intended to be included solely by GenomeSequence.cpp, which
// needs it to compute the MD5 checksum of chromosomes it is building.
//

/* MDDRIVER.C - test driver for MD2, MD4 and MD5
 */

/* Copyright (C) 1990-2, RSA Data Security, Inc. Created 1990. All
rights reserved.

RSA Data Security, Inc. makes no representations concerning either
the merchantability of this software or the suitability of this
software for any particular purpose. It is provided "as is"
without express or implied warranty of any kind.

These notices must be retained in any copies of any part of this
documentation and/or software.
 */

#include <stdio.h>
#include <time.h>
#include <string.h>

/* MD5.H - header file for MD5C.C
 */

/* Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
rights reserved.

License to copy and use this software is granted provided that it
is identified as the "RSA Data Security, Inc. MD5 Message-Digest
Algorithm" in all material mentioning or referencing this software
or this function.

License is also granted to make and use derivative works provided
that such works are identified as "derived from the RSA Data
Security, Inc. MD5 Message-Digest Algorithm" in all material
mentioning or referencing the derived work.

RSA Data Security, Inc. makes no representations concerning either
the merchantability of this software or the suitability of this
software for any particular purpose. It is provided "as is"
without express or implied warranty of any kind.

These notices must be retained in any copies of any part of this
documentation and/or software.
 */

#include <stdint.h>

/* MD5 context. */
typedef struct {
  uint32_t state[4];                                   /* state (ABCD) */
  uint32_t count[2];        /* number of bits, modulo 2^64 (lsb first) */
  unsigned char buffer[64];                         /* input buffer */
} MD5_CTX;

static void MD5Init(MD5_CTX *);
static void MD5Update(MD5_CTX *, unsigned char *, unsigned int);
static void MD5Final(unsigned char [16], MD5_CTX *);


/* MD5C.C - RSA Data Security, Inc., MD5 message-digest algorithm
 */

/* Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
rights reserved.

License to copy and use this software is granted provided that it
is identified as the "RSA Data Security, Inc. MD5 Message-Digest
Algorithm" in all material mentioning or referencing this software
or this function.

License is also granted to make and use derivative works provided
that such works are identified as "derived from the RSA Data
Security, Inc. MD5 Message-Digest Algorithm" in all material
mentioning or referencing the derived work.

RSA Data Security, Inc. makes no representations concerning either
the merchantability of this software or the suitability of this
software for any particular purpose. It is provided "as is"
without express or implied warranty of any kind.

These notices must be retained in any copies of any part of this
documentation and/or software.
 */

/* Constants for MD5Transform routine.
 */

#define S11 7
#define S12 12
#define S13 17
#define S14 22
#define S21 5
#define S22 9
#define S23 14
#define S24 20
#define S31 4
#define S32 11
#define S33 16
#define S34 23
#define S41 6
#define S42 10
#define S43 15
#define S44 21

typedef unsigned char *POINTER;

static void MD5Transform(uint32_t [4], unsigned char [64]);
static void Encode(unsigned char *, uint32_t *, unsigned int);
static void Decode(uint32_t *, unsigned char *, unsigned int);
static void MD5_memcpy(POINTER, POINTER, unsigned int);
static void MD5_memset(POINTER, int, unsigned int);

static unsigned char PADDING[64] = {
  0x80, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};

/* F, G, H and I are basic MD5 functions.
 */
#define F(x, y, z) (((x) & (y)) | ((~x) & (z)))
#define G(x, y, z) (((x) & (z)) | ((y) & (~z)))
#define H(x, y, z) ((x) ^ (y) ^ (z))
#define I(x, y, z) ((y) ^ ((x) | (~z)))

/* ROTATE_LEFT rotates x left n bits.
 */
#define ROTATE_LEFT(x, n) (((x) << (n)) | ((x) >> (32-(n))))

/* FF, GG, HH, and II transformations for rounds 1, 2, 3, and 4.
Rotation is separate from addition to prevent recomputation.
 */
#define FF(a, b, c, d, x, s, ac) { \
 (a) += F ((b), (c), (d)) + (x) + (uint32_t)(ac); \
 (a) = ROTATE_LEFT ((a), (s)); \
 (a) += (b); \
  }
#define GG(a, b, c, d, x, s, ac) { \
 (a) += G ((b), (c), (d)) + (x) + (uint32_t)(ac); \
 (a) = ROTATE_LEFT ((a), (s)); \
 (a) += (b); \
  }
#define HH(a, b, c, d, x, s, ac) { \
 (a) += H ((b), (c), (d)) + (x) + (uint32_t)(ac); \
 (a) = ROTATE_LEFT ((a), (s)); \
 (a) += (b); \
  }
#define II(a, b, c, d, x, s, ac) { \
 (a) += I ((b), (c), (d)) + (x) + (uint32_t)(ac); \
 (a) = ROTATE_LEFT ((a), (s)); \
 (a) += (b); \
  }

/* MD5 initialization. Begins an MD5 operation, writing a new context.
 */
static void MD5Init ( MD5_CTX *context)                                        /* context */
{
  context->count[0] = context->count[1] = 0;
  /* Load magic initialization constants.
*/
  context->state[0] = 0x67452301;
  context->state[1] = 0xefcdab89;
  context->state[2] = 0x98badcfe;
  context->state[3] = 0x10325476;
}

/* MD5 block update operation. Continues an MD5 message-digest
  operation, processing another message block, and updating the
  context.
 */
static void MD5Update (
MD5_CTX *context,                                        /* context */
unsigned char *input,                                /* input block */
unsigned int inputLen)                     /* length of input block */
{
  unsigned int i, index, partLen;

  /* Compute number of bytes mod 64 */
  index = (unsigned int)((context->count[0] >> 3) & 0x3F);

  /* Update number of bits */
  if ((context->count[0] += ((uint32_t)inputLen << 3))
   < ((uint32_t)inputLen << 3))
 context->count[1]++;
  context->count[1] += ((uint32_t)inputLen >> 29);

  partLen = 64 - index;

  /* Transform as many times as possible.
*/
  if (inputLen >= partLen) {
 MD5_memcpy
   ((POINTER)&context->buffer[index], (POINTER)input, partLen);
 MD5Transform (context->state, context->buffer);

 for (i = partLen; i + 63 < inputLen; i += 64)
   MD5Transform (context->state, &input[i]);

 index = 0;
  }
  else
 i = 0;

  /* Buffer remaining input */
  MD5_memcpy
 ((POINTER)&context->buffer[index], (POINTER)&input[i],
  inputLen-i);
}

/* MD5 finalization. Ends an MD5 message-digest operation, writing the
  the message digest and zeroizing the context.
 */
static void MD5Final (
unsigned char digest[16],                         /* message digest */
MD5_CTX *context)                                       /* context */
{
  unsigned char bits[8];
  unsigned int index, padLen;

  /* Save number of bits */
  Encode (bits, context->count, 8);

  /* Pad out to 56 mod 64.
*/
  index = (unsigned int)((context->count[0] >> 3) & 0x3f);
  padLen = (index < 56) ? (56 - index) : (120 - index);
  MD5Update (context, PADDING, padLen);

  /* Append length (before padding) */
  MD5Update (context, bits, 8);

  /* Store state in digest */
  Encode (digest, context->state, 16);

  /* Zeroize sensitive information.
*/
  MD5_memset ((POINTER)context, 0, sizeof (*context));
}

/* MD5 basic transformation. Transforms state based on block.
 */
static void MD5Transform (
uint32_t state[4],
unsigned char block[64])
{
  uint32_t a = state[0], b = state[1], c = state[2], d = state[3], x[16];

  Decode (x, block, 64);

  /* Round 1 */
  FF (a, b, c, d, x[ 0], S11, 0xd76aa478); /* 1 */
  FF (d, a, b, c, x[ 1], S12, 0xe8c7b756); /* 2 */
  FF (c, d, a, b, x[ 2], S13, 0x242070db); /* 3 */
  FF (b, c, d, a, x[ 3], S14, 0xc1bdceee); /* 4 */
  FF (a, b, c, d, x[ 4], S11, 0xf57c0faf); /* 5 */
  FF (d, a, b, c, x[ 5], S12, 0x4787c62a); /* 6 */
  FF (c, d, a, b, x[ 6], S13, 0xa8304613); /* 7 */
  FF (b, c, d, a, x[ 7], S14, 0xfd469501); /* 8 */
  FF (a, b, c, d, x[ 8], S11, 0x698098d8); /* 9 */
  FF (d, a, b, c, x[ 9], S12, 0x8b44f7af); /* 10 */
  FF (c, d, a, b, x[10], S13, 0xffff5bb1); /* 11 */
  FF (b, c, d, a, x[11], S14, 0x895cd7be); /* 12 */
  FF (a, b, c, d, x[12], S11, 0x6b901122); /* 13 */
  FF (d, a, b, c, x[13], S12, 0xfd987193); /* 14 */
  FF (c, d, a, b, x[14], S13, 0xa679438e); /* 15 */
  FF (b, c, d, a, x[15], S14, 0x49b40821); /* 16 */

 /* Round 2 */
  GG (a, b, c, d, x[ 1], S21, 0xf61e2562); /* 17 */
  GG (d, a, b, c, x[ 6], S22, 0xc040b340); /* 18 */
  GG (c, d, a, b, x[11], S23, 0x265e5a51); /* 19 */
  GG (b, c, d, a, x[ 0], S24, 0xe9b6c7aa); /* 20 */
  GG (a, b, c, d, x[ 5], S21, 0xd62f105d); /* 21 */
  GG (d, a, b, c, x[10], S22,  0x2441453); /* 22 */
  GG (c, d, a, b, x[15], S23, 0xd8a1e681); /* 23 */
  GG (b, c, d, a, x[ 4], S24, 0xe7d3fbc8); /* 24 */
  GG (a, b, c, d, x[ 9], S21, 0x21e1cde6); /* 25 */
  GG (d, a, b, c, x[14], S22, 0xc33707d6); /* 26 */
  GG (c, d, a, b, x[ 3], S23, 0xf4d50d87); /* 27 */
  GG (b, c, d, a, x[ 8], S24, 0x455a14ed); /* 28 */
  GG (a, b, c, d, x[13], S21, 0xa9e3e905); /* 29 */
  GG (d, a, b, c, x[ 2], S22, 0xfcefa3f8); /* 30 */
  GG (c, d, a, b, x[ 7], S23, 0x676f02d9); /* 31 */
  GG (b, c, d, a, x[12], S24, 0x8d2a4c8a); /* 32 */

  /* Round 3 */
  HH (a, b, c, d, x[ 5], S31, 0xfffa3942); /* 33 */
  HH (d, a, b, c, x[ 8], S32, 0x8771f681); /* 34 */
  HH (c, d, a, b, x[11], S33, 0x6d9d6122); /* 35 */
  HH (b, c, d, a, x[14], S34, 0xfde5380c); /* 36 */
  HH (a, b, c, d, x[ 1], S31, 0xa4beea44); /* 37 */
  HH (d, a, b, c, x[ 4], S32, 0x4bdecfa9); /* 38 */
  HH (c, d, a, b, x[ 7], S33, 0xf6bb4b60); /* 39 */
  HH (b, c, d, a, x[10], S34, 0xbebfbc70); /* 40 */
  HH (a, b, c, d, x[13], S31, 0x289b7ec6); /* 41 */
  HH (d, a, b, c, x[ 0], S32, 0xeaa127fa); /* 42 */
  HH (c, d, a, b, x[ 3], S33, 0xd4ef3085); /* 43 */
  HH (b, c, d, a, x[ 6], S34,  0x4881d05); /* 44 */
  HH (a, b, c, d, x[ 9], S31, 0xd9d4d039); /* 45 */
  HH (d, a, b, c, x[12], S32, 0xe6db99e5); /* 46 */
  HH (c, d, a, b, x[15], S33, 0x1fa27cf8); /* 47 */
  HH (b, c, d, a, x[ 2], S34, 0xc4ac5665); /* 48 */

  /* Round 4 */
  II (a, b, c, d, x[ 0], S41, 0xf4292244); /* 49 */
  II (d, a, b, c, x[ 7], S42, 0x432aff97); /* 50 */
  II (c, d, a, b, x[14], S43, 0xab9423a7); /* 51 */
  II (b, c, d, a, x[ 5], S44, 0xfc93a039); /* 52 */
  II (a, b, c, d, x[12], S41, 0x655b59c3); /* 53 */
  II (d, a, b, c, x[ 3], S42, 0x8f0ccc92); /* 54 */
  II (c, d, a, b, x[10], S43, 0xffeff47d); /* 55 */
  II (b, c, d, a, x[ 1], S44, 0x85845dd1); /* 56 */
  II (a, b, c, d, x[ 8], S41, 0x6fa87e4f); /* 57 */
  II (d, a, b, c, x[15], S42, 0xfe2ce6e0); /* 58 */
  II (c, d, a, b, x[ 6], S43, 0xa3014314); /* 59 */
  II (b, c, d, a, x[13], S44, 0x4e0811a1); /* 60 */
  II (a, b, c, d, x[ 4], S41, 0xf7537e82); /* 61 */
  II (d, a, b, c, x[11], S42, 0xbd3af235); /* 62 */
  II (c, d, a, b, x[ 2], S43, 0x2ad7d2bb); /* 63 */
  II (b, c, d, a, x[ 9], S44, 0xeb86d391); /* 64 */

  state[0] += a;
  state[1] += b;
  state[2] += c;
  state[3] += d;

  /* Zeroize sensitive information.
*/
  MD5_memset ((POINTER)x, 0, sizeof (x));
}

/* Encodes input (uint32_t) into output (unsigned char). Assumes len is
  a multiple of 4.
 */
static void Encode (
unsigned char *output,
uint32_t *input,
unsigned int len)
{
  unsigned int i, j;

  for (i = 0, j = 0; j < len; i++, j += 4) {
 output[j] = (unsigned char)(input[i] & 0xff);
 output[j+1] = (unsigned char)((input[i] >> 8) & 0xff);
 output[j+2] = (unsigned char)((input[i] >> 16) & 0xff);
 output[j+3] = (unsigned char)((input[i] >> 24) & 0xff);
  }
}

/* Decodes input (unsigned char) into output (uint32_t). Assumes len is
  a multiple of 4.
 */
static void Decode (
uint32_t *output,
unsigned char *input,
unsigned int len)
{
  unsigned int i, j;

  for (i = 0, j = 0; j < len; i++, j += 4)
 output[i] = ((uint32_t)input[j]) | (((uint32_t)input[j+1]) << 8) |
   (((uint32_t)input[j+2]) << 16) | (((uint32_t)input[j+3]) << 24);
}

/* Note: Replace "for loop" with standard memcpy if possible.
 */

static void MD5_memcpy (
POINTER output,
POINTER input,
unsigned int len)
{
  unsigned int i;

  for (i = 0; i < len; i++)
       output[i] = input[i];
}

/* Note: Replace "for loop" with standard memset if possible.
 */
static void MD5_memset (
POINTER output,
int value,
unsigned int len)
{
  unsigned int i;

  for (i = 0; i < len; i++)
 ((char *)output)[i] = (char)value;
}