C++ (Cpp) alurusort Examples

Example #1

File: shangsuf.c Project: AlexWoroschilow/wurst-alphabet

  Suffixarray*
constructSufArr(void *space, 
    CharSequence **s, 
    Uint len, 
    FAlphabet* alphabet)
{

  Uint i, numofsuffixes,
  *sorted, 
  *inv_suftab;
  char **suffixptr;
  MultiCharSeq *mseq; 
  Suffixarray *arr;

  mseq = concatCharSequences(space, s, len, (char)254, (char)127);
  numofsuffixes = (mseq->totallength - mseq->numofsequences)+1; 

  //printf("md5: %s\n", MD5((unsigned char*)"f**k",4,NULL));
  fprintf(stderr, "alphabet of size (%d): %s\n", mseq->mapsize, mseq->map);
  //fprintf(stderr, "allocating space for %d suffixes (%d bytes)\n", numofsuffixes, 2*numofsuffixes*sizeof(Uint));
  inv_suftab = ALLOCMEMORY(space, NULL, Uint , numofsuffixes);
  arr = ALLOCMEMORY(space, NULL, Suffixarray, 1);

  fprintf(stderr, "constructing suftab.\n");
  suffixptr = getSuffixPtr(space, mseq, (char)254, (char)127);

  //mseq->sequences[numofsuffixes-1]=0; 
  sorted = alurusort(space, mseq->sequences, &(numofsuffixes));
  //  mseq->sequences[numofsuffixes-1]=save;

  /*  sorted = quickSortMultikey (space, suffixptr, numofsuffixes, 
      cmpCharSequence, numofsuffixes-1, NULL);     
      */
  fprintf(stderr, "constructing inv_suftab.\n");
  for (i=0; i < numofsuffixes; i++) {
    inv_suftab[sorted[i]]=i;
  }

  arr->seq = mseq;
  arr->numofsuffixes = numofsuffixes;
  arr->suffixptr = suffixptr;
  arr->suftab = sorted;
  arr->inv_suftab = inv_suftab;

  return arr;
}

Example #2

File: sufarray.c Project: spundhir/RNA-Seq

  Suffixarray*
constructSufArr(void *space, 
    CharSequence **s, 
    Uint len, 
    FAlphabet* alphabet,
    unsigned char silent)
{

  Uint i, numofsuffixes,
  *sorted, 
  *inv_suftab;
  MultiCharSeq *mseq; 
  Suffixarray *arr;
  unsigned char *temp,
                *mdfive=NULL;


  
  mseq = concatCharSequences(space, s, len, (char)126, (char)127);
  numofsuffixes = mseq->totallength;
  mdfive  = ALLOCMEMORY(space, NULL, char, 16);
  temp = MD5R((unsigned char*)mseq->sequences, numofsuffixes, NULL);
  
  
  memmove(mdfive, temp, 16);


  if(!silent) NFO("alphabet of size (%d): %s\n", mseq->mapsize, mseq->map);
  if(!silent) NFO("size of db sequence: %u\n", numofsuffixes);
  inv_suftab = ALLOCMEMORY(space, NULL, Uint , numofsuffixes);
  arr = ALLOCMEMORY(space, NULL, Suffixarray, 1);

  if(!silent) MSG("constructing suftab.\n");

#ifdef SUF_MKQUICKSORT
  sorted = quickSortMultikey (space, mseq->sequences, numofsuffixes, 
      cmpCharSequence, numofsuffixes-1, NULL);     
#else
  sorted = alurusort(space, mseq->sequences, 
      &(numofsuffixes));
#endif

  if (!silent)NFO("constructing inv_suftab (%u).\n", numofsuffixes);
  for (i=0; i < numofsuffixes; i++) {
    if (sorted[i] > numofsuffixes) fprintf(stderr, "construction error? %u: %u\n",i, sorted[i]);
    inv_suftab[sorted[i]]=i;
  }
  if (!silent)MSG("inv_suftab constructed.\n");

  arr->seq = mseq;
  arr->numofsuffixes = numofsuffixes;
  arr->suftab = sorted;
  arr->inv_suftab = inv_suftab;
  arr->mdfive = mdfive;
  arr->lcpctab = NULL;
  arr->llvtab = NULL;
  
  arr->id = NULL;
  arr->idvtab = NULL;
  arr->chldtab = NULL;
  arr->bcktab = NULL;

  arr->suflink = NULL;
  arr->suflink_l = NULL;
  arr->suflink_r = NULL;
  arr->llint = 1;
  return arr;
}