#ifdef _cplusplus
extern "C" {
#endif
#include "kmer_hash.h"




 static int crc_table[256] = {
  0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419,
  0x706af48f, 0xe963a535, 0x9e6495a3, 0x0edb8832, 0x79dcb8a4,
  0xe0d5e91e, 0x97d2d988, 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07,
  0x90bf1d91, 0x1db71064, 0x6ab020f2, 0xf3b97148, 0x84be41de,
  0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7, 0x136c9856,
  0x646ba8c0, 0xfd62f97a, 0x8a65c9ec, 0x14015c4f, 0x63066cd9,
  0xfa0f3d63, 0x8d080df5, 0x3b6e20c8, 0x4c69105e, 0xd56041e4,
  0xa2677172, 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b,
  0x35b5a8fa, 0x42b2986c, 0xdbbbc9d6, 0xacbcf940, 0x32d86ce3,
  0x45df5c75, 0xdcd60dcf, 0xabd13d59, 0x26d930ac, 0x51de003a,
  0xc8d75180, 0xbfd06116, 0x21b4f4b5, 0x56b3c423, 0xcfba9599,
  0xb8bda50f, 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924,
  0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d, 0x76dc4190,
  0x01db7106, 0x98d220bc, 0xefd5102a, 0x71b18589, 0x06b6b51f,
  0x9fbfe4a5, 0xe8b8d433, 0x7807c9a2, 0x0f00f934, 0x9609a88e,
  0xe10e9818, 0x7f6a0dbb, 0x086d3d2d, 0x91646c97, 0xe6635c01,
  0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e, 0x6c0695ed,
  0x1b01a57b, 0x8208f4c1, 0xf50fc457, 0x65b0d9c6, 0x12b7e950,
  0x8bbeb8ea, 0xfcb9887c, 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3,
  0xfbd44c65, 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2,
  0x4adfa541, 0x3dd895d7, 0xa4d1c46d, 0xd3d6f4fb, 0x4369e96a,
  0x346ed9fc, 0xad678846, 0xda60b8d0, 0x44042d73, 0x33031de5,
  0xaa0a4c5f, 0xdd0d7cc9, 0x5005713c, 0x270241aa, 0xbe0b1010,
  0xc90c2086, 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f,
  0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4, 0x59b33d17,
  0x2eb40d81, 0xb7bd5c3b, 0xc0ba6cad, 0xedb88320, 0x9abfb3b6,
  0x03b6e20c, 0x74b1d29a, 0xead54739, 0x9dd277af, 0x04db2615,
  0x73dc1683, 0xe3630b12, 0x94643b84, 0x0d6d6a3e, 0x7a6a5aa8,
  0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1, 0xf00f9344,
  0x8708a3d2, 0x1e01f268, 0x6906c2fe, 0xf762575d, 0x806567cb,
  0x196c3671, 0x6e6b06e7, 0xfed41b76, 0x89d32be0, 0x10da7a5a,
  0x67dd4acc, 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5,
  0xd6d6a3e8, 0xa1d1937e, 0x38d8c2c4, 0x4fdff252, 0xd1bb67f1,
  0xa6bc5767, 0x3fb506dd, 0x48b2364b, 0xd80d2bda, 0xaf0a1b4c,
  0x36034af6, 0x41047a60, 0xdf60efc3, 0xa867df55, 0x316e8eef,
  0x4669be79, 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236,
  0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f, 0xc5ba3bbe,
  0xb2bd0b28, 0x2bb45a92, 0x5cb36a04, 0xc2d7ffa7, 0xb5d0cf31,
  0x2cd99e8b, 0x5bdeae1d, 0x9b64c2b0, 0xec63f226, 0x756aa39c,
  0x026d930a, 0x9c0906a9, 0xeb0e363f, 0x72076785, 0x05005713,
  0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38, 0x92d28e9b,
  0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21, 0x86d3d2d4, 0xf1d4e242,
  0x68ddb3f8, 0x1fda836e, 0x81be16cd, 0xf6b9265b, 0x6fb077e1,
  0x18b74777, 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c,
  0x8f659eff, 0xf862ae69, 0x616bffd3, 0x166ccf45, 0xa00ae278,
  0xd70dd2ee, 0x4e048354, 0x3903b3c2, 0xa7672661, 0xd06016f7,
  0x4969474d, 0x3e6e77db, 0xaed16a4a, 0xd9d65adc, 0x40df0b66,
  0x37d83bf0, 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9,
  0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6, 0xbad03605,
  0xcdd70693, 0x54de5729, 0x23d967bf, 0xb3667a2e, 0xc4614ab8,
  0x5d681b02, 0x2a6f2b94, 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b,
  0x2d02ef8d
 };


# line 95 "kmer_hash.dy"
int crc32(int crc, const char *buf, int len)
{
    if (buf == NULL) return 0;

    crc = crc ^ 0xffffffff;
    while(len--){
	crc = crc_table[((int)crc ^ (*buf++)) & 0xff] ^ (crc >> 8);
    }
    return crc ^ 0xffffffff;
}



# line 108 "kmer_hash.dy"
KmerIndexInterface * new_KmerHashIndex(int kmer_size)
{
  KmerIndexInterface * out;
  KmerHashIndex * khi;


  khi = malloc(sizeof(KmerHashIndex));
  khi->bucket = calloc(KMER_HASH_BUCKETS,sizeof(KmerHashBucket));
  if( khi->bucket == NULL ) {
    warn("could not allocate hash table of size %ld\n",KMER_HASH_BUCKETS);
    return NULL;
  }
  khi->min_kmer = 0xffffffff;
  khi->max_kmer = 0x00000000;

  out = malloc(sizeof(KmerIndexInterface));

  out->retrieve_by_kmer  = retrieve_by_kmer_KmerHashIndex;
  out->insert_by_kmer    = insert_by_kmer_KmerHashIndex;
  out->free_handle       = free_KmerHashIndex;
  out->next_filled_kmer  = next_filled_kmer_KmerHashIndex;

  out->handle = (void*) khi;
  out->kmer_size = kmer_size;

  return out;

}




# line 140 "kmer_hash.dy"
kmer_t hash_kmer(kmer_t kmer)
{
  kmer_t hash = kmer;

/*
  kmer >>= 24;
  hash ^= kmer;
*/

/*
  kmer <<= 5;
  hash ^= kmer;
  kmer <<= 5;
  hash ^= kmer;
  kmer <<= 5;
  hash ^= kmer;
  kmer <<= 5;
  hash ^= kmer;
  kmer <<= 5;
  hash ^= kmer;
*/

/*
  kmer >>= 28;
  hash ^= kmer;
*/

  hash = crc32(0, (char*)&kmer, sizeof(kmer_t));

  hash &= KMER_HASH_MASK;

  return hash;
}

# line 174 "kmer_hash.dy"
void * retrieve_by_kmer_KmerHashIndex(void * handle,kmer_t kmer)
{
  kmer_t hashval = hash_kmer(kmer);
  KmerHashIndex *khi = (KmerHashIndex*) handle;
  KmerHashBucket *khb;
  int i;
  assert(khi);
  khb = &khi->bucket[hashval];

  if(!khb->index) return NULL;

  for(i = 0; i < khb->length; ++i){
    if(khb->kmer[i] == kmer){
      return khb->index[i];
    }
  }

  return NULL;
}



# line 196 "kmer_hash.dy"
kmer_t next_filled_kmer_KmerHashIndex(void * handle,kmer_t kmer)
{
  kmer_t hashval;
  KmerHashIndex *khi = (KmerHashIndex*) handle;
  KmerHashBucket *khb;
  int i;
  assert(khi);


  /* starting bucket */
  if( kmer == -1 ) {
    for(i=0;i<KMER_HASH_BUCKETS;i++) {
      if( khi->bucket[i].index != NULL ) {
	return khi->bucket[i].kmer[0];
      }
    }
  }

  /* else we've got a real one */


  hashval = hash_kmer(kmer);

  khb = &khi->bucket[hashval];
  assert(khb != NULL);
  for(i=0;i<khb->length;i++) {
    if( kmer == khb->kmer[i] ) {
      break;
    }
  }

  /* as we give out these numbers, they must be here! */
  assert(i < khb->length);
  if( i+1 == khb->length ) {
    /* next hashval needed */
    for(i=hashval+1;i<KMER_HASH_BUCKETS;i++) {
      if( khi->bucket[i].index != NULL ) {
	return khi->bucket[i].kmer[0];
      }
    } 
    /* out of buckets - return -1 */
    return -1;
  } else {
    /* return next position in this bucket */
    return khb->kmer[i+1];
  }


}


# line 247 "kmer_hash.dy"
boolean insert_by_kmer_KmerHashIndex(void * handle,kmer_t kmer,void * poi)
{
  kmer_t hashval = hash_kmer(kmer);
  KmerHashIndex *khi = (KmerHashIndex*) handle;
  KmerHashBucket *khb;
  int i;
  assert(khi);

  if(kmer > khi->max_kmer) khi->max_kmer = kmer;
  if(kmer < khi->min_kmer) khi->min_kmer = kmer;

  khb = &khi->bucket[hashval];

  if(khb->index == NULL){
    khb->index = (void**)malloc(sizeof(void*)*8);
    if(khb->index == NULL){
      fprintf(stderr, "Out of memory\n");
      exit(1);
    }
    khb->kmer  = (kmer_t*)malloc(sizeof(kmer_t)*8);
    if(khb->kmer == NULL){
      fprintf(stderr, "Out of memory\n");
      exit(1);
    }
    khb->buflen = 8;
  }

  if(khb->length >= khb->buflen){
    khb->index = (void**)realloc(khb->index, sizeof(void*)*(khb->buflen*2));
    if(khb->index == NULL){
      fprintf(stderr, "Out of memory\n");
      exit(1);
    }
    khb->kmer  = (kmer_t*)realloc(khb->kmer, sizeof(kmer_t)*(khb->buflen*2));
    if(khb->kmer == NULL){
      fprintf(stderr, "Out of memory\n");
      exit(1);
    }
    khb->buflen *= 2;
  }

  khb->kmer[khb->length] = kmer;
  khb->index[khb->length] = poi;
  khb->length++;

  return TRUE;
}


# line 296 "kmer_hash.dy"
void free_KmerHashIndex(void * handle)
{
  int i;
  int lenhist[10];
  KmerHashIndex *khi = (KmerHashIndex*) handle;
  KmerHashBucket *khb;
  assert(khi);

  for(i = 0; i < 10; ++i) lenhist[i] = 0;

  for(i = 0; i < KMER_HASH_BUCKETS; ++i){
    khb = &khi->bucket[i];
    if(khb->length >= 10){
      lenhist[9]++;
    } else {
      lenhist[khb->length]++;
    }
    if(khb->index) free(khb->index);
    if(khb->kmer) free(khb->kmer);
  }
  free(khi->bucket);

  fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer);
  fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer);
  free(khi);

  for(i = 0; i < 9; ++i){
    fprintf(stderr, "%2d:%8d\n", i, lenhist[i]);
  }
  fprintf(stderr, "9+:%8d\n", lenhist[9]);

  return;
}
# line 305 "kmer_hash.c"

#ifdef _cplusplus
}
#endif
