Commit ca4b5b23 authored by Boris Lukačovič's avatar Boris Lukačovič
Browse files

EDIT: config for output redirect

parent 7cff4fc6

Hash/src/config.cpp

+659 −505

File changed.

Preview size limit exceeded, changes collapsed.

Hash/src/user.cpp

+267 −236
Original line number Diff line number Diff line
@@ -9,27 +9,22 @@ 


long int max_dimension = -1; // used for restriction on dimensionality of vector data (used in i.e. print and distance functions).





void restrict_dimension(long int _max_dim)

{

  max_dimension = _max_dim;

}





//********************************************************

//********************************************************

// vector data read, print, distance functions, structures

//********************************************************

//********************************************************





T_DISTANCE get_max_distance_float_vector()

{

  return MAXIMUM_DISTANCE;

}







T_DISTANCE dist_func_L1_float_vector(void *p1, long int p1_len, void *p2, long int p2_len, T_DISTANCE threshold)

{

  // manhattan
@@ -46,7 +41,8 @@ T_DISTANCE dist_func_L1_float_vector(void *p1, long int p1_len, void *p2, long i 
  d1 = (float *)p1;

  d2 = (float *)p2;



  for(long int i = 0; i < dim; i++) {

  for (long int i = 0; i < dim; i++)

  {

    if (d1[i] < d2[i])

      ret += (d2[i] - d1[i]);

    else
@@ -56,9 +52,6 @@ T_DISTANCE dist_func_L1_float_vector(void *p1, long int p1_len, void *p2, long i 
  return ret;

}









T_DISTANCE dist_func_L2_float_vector(void *p1, long int p1_len, void *p2, long int p2_len, T_DISTANCE threshold)

{

  float *d1, *d2;
@@ -75,7 +68,8 @@ T_DISTANCE dist_func_L2_float_vector(void *p1, long int p1_len, void *p2, long i 
  d1 = (float *)p1;

  d2 = (float *)p2;



  for(long int i = 0; i < dim; i++) {

  for (long int i = 0; i < dim; i++)

  {

    diff = d2[i] - d1[i];

    ret += diff * diff;

  }
@@ -85,9 +79,6 @@ T_DISTANCE dist_func_L2_float_vector(void *p1, long int p1_len, void *p2, long i 
  return ret;

}









int read_obj_func_float_vector(FILE *f_in, long int dimensions, P_VOID &data, long int &data_len)

{

  // this functions reads object's data from file f_in
@@ -103,14 +94,16 @@ int read_obj_func_float_vector(FILE *f_in, long int dimensions, P_VOID &data, lo 
  data = malloc(data_len);

  d = (float *)data;



  while ( (!feof(f_in)) && (i < dimensions) ) {

  while ((!feof(f_in)) && (i < dimensions))

  {

    if (fscanf(f_in, "%f", &tmp) == EOF)

      break;

    d[i] = tmp;

    ++i;

  }



  if (i < dimensions) {

  if (i < dimensions)

  {

    if (data)

      free(data);

    data = NULL;
@@ -120,9 +113,6 @@ int read_obj_func_float_vector(FILE *f_in, long int dimensions, P_VOID &data, lo 
  return 0;

}









void print_obj_func_float_vector(void *data, long int data_len, FILE *f_out, unsigned int delim, const char *txt_pre, long int obj_id, int is_colored, const char *txt_post)

{

  // data, data_len - data of object
@@ -133,7 +123,8 @@ void print_obj_func_float_vector(void *data, long int data_len, FILE *f_out, uns 
  float *d;

  long int dim;



  if (txt_pre) {

  if (txt_pre)

  {

    const char *c;

    c = strchr(txt_pre, '%');

    if (c == NULL || c[1] != 'c')
@@ -147,7 +138,8 @@ void print_obj_func_float_vector(void *data, long int data_len, FILE *f_out, uns 
  if (max_dimension != -1 && dim > max_dimension)

    dim = max_dimension;



  if (dim) {

  if (dim)

  {

    fprintf(f_out, "%f", d[0]);

    for (long int i = 1; i < dim; i++)

      fprintf(f_out, "%c%f", delim, d[i]);
@@ -157,33 +149,29 @@ void print_obj_func_float_vector(void *data, long int data_len, FILE *f_out, uns 
    fputs(txt_post, f_out);

}







//********************************************************

//********************************************************

// URL read, print, distance functions, structures

//********************************************************

//********************************************************



struct t_url {

struct t_url

{

  long int next_off;

  char url[1];

};



struct t_url_data {

struct t_url_data

{

  long int cnt;

  t_url urls[1];

};







T_DISTANCE get_max_distance_urls()

{

  return (T_DISTANCE)1;

}







T_DISTANCE dist_func_url_sets(void *p1, long int p1_len, void *p2, long int p2_len, T_DISTANCE threshold)

{

// #define UNSORTED_VERSION
@@ -198,7 +186,8 @@ T_DISTANCE dist_func_url_sets(void *p1, long int p1_len, void *p2, long int p2_l 


  cnt_p1 = ((t_url_data *)p1)->cnt;

  cnt_p2 = ((t_url_data *)p2)->cnt;

  if (cnt_p1 < cnt_p2) {

  if (cnt_p1 < cnt_p2)

  {

    void *tmp = p1;

    long int ltmp = p1_len;

    p1 = p2;
@@ -210,26 +199,30 @@ T_DISTANCE dist_func_url_sets(void *p1, long int p1_len, void *p2, long int p2_l 
    cnt_p2 = ltmp;

  }





  // evaluate size of intersect of p1 and p2

  off1 = (long int *)(((t_url_data *)p1)->urls);



  for(i = 0; i < cnt_p1; i++) {

  for (i = 0; i < cnt_p1; i++)

  {

    url1 = (char *)off1 + sizeof(long int);



    off2 = (long int *)(((t_url_data *)p1)->urls);

    for (j = 0; j < i; j++) {

    for (j = 0; j < i; j++)

    {

      url2 = (char *)off2 + sizeof(long int);

      if (strcmp(url1, url2) == 0)

        break;

      off2 = (long int *)((char *)p1 + *off2);

    }



    if (j == i) {         // the same url was not found in p1 object

    if (j == i)

    { // the same url was not found in p1 object

      off2 = (long int *)(((t_url_data *)p2)->urls);

      for (j = 0; j < cnt_p2; j++) {

      for (j = 0; j < cnt_p2; j++)

      {

        url2 = (char *)off2 + sizeof(long int);

        if (strcmp(url1, url2) == 0) {

        if (strcmp(url1, url2) == 0)

        {

          ++cnt_inter;

          break;

        }
@@ -243,11 +236,13 @@ T_DISTANCE dist_func_url_sets(void *p1, long int p1_len, void *p2, long int p2_l 
  // evaluate size of union of p1 and p2

  off1 = (long int *)(((t_url_data *)p1)->urls);



  for(i = 0; i < cnt_p1; i++) {

  for (i = 0; i < cnt_p1; i++)

  {

    url1 = (char *)off1 + sizeof(long int);

    off2 = (long int *)(((t_url_data *)p1)->urls);



    for (j = 0; j < i; j++) {

    for (j = 0; j < i; j++)

    {

      url2 = (char *)off2 + sizeof(long int);

      if (strcmp(url1, url2) == 0)

        break;
@@ -261,23 +256,27 @@ T_DISTANCE dist_func_url_sets(void *p1, long int p1_len, void *p2, long int p2_l 


  off1 = (long int *)(((t_url_data *)p2)->urls);



  for(i = 0; i < cnt_p2; i++) {

  for (i = 0; i < cnt_p2; i++)

  {

    url1 = (char *)off1 + sizeof(long int);



    // search in p2

    off2 = (long int *)(((t_url_data *)p2)->urls);



    for (j = 0; j < i; j++) {

    for (j = 0; j < i; j++)

    {

      url2 = (char *)off2 + sizeof(long int);

      if (strcmp(url1, url2) == 0)

        break;

      off2 = (long int *)((char *)p2 + *off2);

    }

    if (j == i) {

    if (j == i)

    {

      // search in p1

      off2 = (long int *)(((t_url_data *)p1)->urls);



      for (j = 0; j < cnt_p1; j++) {

      for (j = 0; j < cnt_p1; j++)

      {

        url2 = (char *)off2 + sizeof(long int);

        if (strcmp(url1, url2) == 0)

          break;
@@ -315,20 +314,24 @@ T_DISTANCE dist_func_url_sets(void *p1, long int p1_len, void *p2, long int p2_l 
  url2 = (char *)off2 + sizeof(long int);

  i = 0;

  j = 0;

  while (i < cnt_p1 && j < cnt_p2) {

  while (i < cnt_p1 && j < cnt_p2)

  {

    cmp = strcmp(url1, url2);

  	if (cmp == 0) {				// url1 and url2 are the same

    if (cmp == 0)

    { // url1 and url2 are the same

      ++cnt_inter;

      off1 = (long int *)((char *)p1 + *off1);

      url1 = (char *)off1 + sizeof(long int);

      ++i;

    }

  	else if (cmp < 0) {		// url1 is less than url2

    else if (cmp < 0)

    { // url1 is less than url2

      off1 = (long int *)((char *)p1 + *off1);

      url1 = (char *)off1 + sizeof(long int);

      ++i;

    }

  	else { // cmp > 0			// url2 is less than url1

    else

    { // cmp > 0			// url2 is less than url1

      off2 = (long int *)((char *)p2 + *off2);

      url2 = (char *)off2 + sizeof(long int);

      ++j;
@@ -345,8 +348,6 @@ T_DISTANCE dist_func_url_sets(void *p1, long int p1_len, void *p2, long int p2_l 
#endif

}







void print_obj_func_urls(void *data, long int data_len, FILE *f_out, unsigned int delim,

                         const char *txt_pre, long int obj_id, int is_colored, const char *txt_post)

{
@@ -359,7 +360,8 @@ void print_obj_func_urls(void *data, long int data_len, FILE *f_out, unsigned in 
  char *url;

  long int *off;



  if (txt_pre) {

  if (txt_pre)

  {

    const char *c;

    c = strchr(txt_pre, '%');

    if (c == NULL || c[1] != 'c')
@@ -368,13 +370,13 @@ void print_obj_func_urls(void *data, long int data_len, FILE *f_out, unsigned in 
      fprintf(f_out, txt_pre, (is_colored) ? '*' : ' ', obj_id);

  }





  cnt = ((t_url_data *)data)->cnt;

  fprintf(f_out, "%ld", cnt);



  off = (long int *)(((t_url_data *)data)->urls);



  for(long int i = 0; i < cnt; i++) {

  for (long int i = 0; i < cnt; i++)

  {

    url = (char *)off + sizeof(long int);

    fputc(delim, f_out);

    fputs(url, f_out);
@@ -385,8 +387,6 @@ void print_obj_func_urls(void *data, long int data_len, FILE *f_out, unsigned in 
    fputs(txt_post, f_out);

}







int read_obj_func_urls(FILE *f_in, long int dimensions, P_VOID &data, long int &data_len)

{

  // this functions reads object's data from file f_in
@@ -400,13 +400,15 @@ int read_obj_func_urls(FILE *f_in, long int dimensions, P_VOID &data, long int & 
  char *url;

  long int *off;



  if (feof(f_in)) {

  if (feof(f_in))

  {

    data = NULL;

    data_len = 0L;

    return 1;

  }



  if (fscanf(f_in, "%ld", &cnt) == EOF) {

  if (fscanf(f_in, "%ld", &cnt) == EOF)

  {

    data = NULL;

    data_len = 0L;

    return 1;
@@ -416,18 +418,18 @@ int read_obj_func_urls(FILE *f_in, long int dimensions, P_VOID &data, long int & 
  allocated = 64 * 1024L;

  data = malloc(allocated);







  data_len = sizeof(long int);



  ((t_url_data *)data)->cnt = cnt; // save count of urls

  url = (char *)&(((t_url_data *)data)->urls);



  for (long int i = 0; i < cnt; i++) {    // read individual urls

  for (long int i = 0; i < cnt; i++)

  { // read individual urls

    off = (long int *)url;

    url += sizeof(long int);

    data_len += sizeof(long int);

    while ((c = fgetc(f_in)) != ' ' && c != EOF && c != '\r' && c != '\n') {

    while ((c = fgetc(f_in)) != ' ' && c != EOF && c != '\r' && c != '\n')

    {

      url[0] = c;

      ++url;

      ++data_len;
@@ -436,7 +438,8 @@ int read_obj_func_urls(FILE *f_in, long int dimensions, P_VOID &data, long int & 
    ++url;

    ++data_len;

    *off = url - (char *)data; // set offset

    if (allocated - data_len < 1024) {      // increase allocated memory

    if (allocated - data_len < 1024)

    { // increase allocated memory

      long int l_off, l_url;



      l_off = (char *)off - (char *)data;
@@ -452,23 +455,17 @@ int read_obj_func_urls(FILE *f_in, long int dimensions, P_VOID &data, long int & 
  return 0;

}







//********************************************************

//********************************************************

// TEXT read, print, distance functions, structures

//********************************************************

//********************************************************







T_DISTANCE get_max_distance_text()

{

  return MAXIMUM_DISTANCE;

}







T_DISTANCE dist_func_text(void *p1, long int p1_len, void *p2, long int p2_len, T_DISTANCE threshold)

{

  int *d;          // pointer to vector
@@ -487,9 +484,11 @@ T_DISTANCE dist_func_text(void *p1, long int p1_len, void *p2, long int p2_len, 
  --p2_len;



  // aproximate distance

  if (threshold != UNUSED_DISTANCE) {

  if (threshold != UNUSED_DISTANCE)

  {

    dist = (T_DISTANCE)fabs(p1_len - p2_len);

    if (threshold < dist) { // dist is the minimum bound, the edit distance cannot be lower

    if (threshold < dist)

    { // dist is the minimum bound, the edit distance cannot be lower

#ifdef HASH_DEBUG

      fprintf(stderr, "%8.2f < %8.2f\n", threshold, dist);

#endif
@@ -501,10 +500,12 @@ T_DISTANCE dist_func_text(void *p1, long int p1_len, void *p2, long int p2_len, 


  // Step 1



  if (p1_len <= 0) {

  if (p1_len <= 0)

  {

    return p2_len;

  }

  if (p2_len <= 0) {

  if (p2_len <= 0)

  {

    return p1_len;

  }

  d = (int *)malloc((p2_len + 1) * sizeof(int));
@@ -517,7 +518,8 @@ T_DISTANCE dist_func_text(void *p1, long int p1_len, void *p2, long int p2_len, 
  // Step 3

  s_i = (char *)p1;



  for (i = 1; i <= p1_len; i++) {

  for (i = 1; i <= p1_len; i++)

  {



    d[0] = i;

    diag_prev = i - 1;
@@ -525,7 +527,8 @@ T_DISTANCE dist_func_text(void *p1, long int p1_len, void *p2, long int p2_len, 
    // Step 4

    t_j = (char *)p2;



    for (j = 1; j <= p2_len; j++) {

    for (j = 1; j <= p2_len; j++)

    {



      // Step 5
@@ -559,8 +562,6 @@ T_DISTANCE dist_func_text(void *p1, long int p1_len, void *p2, long int p2_len, 
  return dist;

}







T_DISTANCE dist_func_text_length(void *p1, long int p1_len, void *p2, long int p2_len, T_DISTANCE threshold)

{

  if (p1_len > p2_len)
@@ -569,8 +570,6 @@ T_DISTANCE dist_func_text_length(void *p1, long int p1_len, void *p2, long int p 
    return p2_len - p1_len;

}







void print_obj_func_text(void *data, long int data_len, FILE *f_out, unsigned int delim, const char *txt_pre, long int obj_id, int is_colored, const char *txt_post)

{

  // data, data_len - data of object
@@ -578,7 +577,8 @@ void print_obj_func_text(void *data, long int data_len, FILE *f_out, unsigned in 
  // txt - additional comment, it's printed out before object's data, this text is used as formating argument to printf function

  // obj_id - this parameter is used as a parameter to printf function together with txt parameter (%ld can be used in txt for priting out)

  // is_colored - this parameter indicates whether the object is colored (1) or not (0) (for details see self-similarity join algo)

  if (txt_pre) {

  if (txt_pre)

  {

    const char *c;

    c = strchr(txt_pre, '%');

    if (c == NULL || c[1] != 'c')
@@ -587,15 +587,12 @@ void print_obj_func_text(void *data, long int data_len, FILE *f_out, unsigned in 
      fprintf(f_out, txt_pre, (is_colored) ? '*' : ' ', obj_id);

  }





  fputs((char *)data, f_out);



  if (txt_post)

    fputs(txt_post, f_out);

}







int read_obj_func_text(FILE *f_in, long int dimensions, P_VOID &data, long int &data_len)

{

  // this functions reads object's data from file f_in
@@ -607,7 +604,8 @@ int read_obj_func_text(FILE *f_in, long int dimensions, P_VOID &data, long int & 
  char c;

  char *txt;



  if (feof(f_in)) {

  if (feof(f_in))

  {

    data = NULL;

    data_len = 0L;

    return 1;
@@ -618,16 +616,19 @@ int read_obj_func_text(FILE *f_in, long int dimensions, P_VOID &data, long int & 
  data_len = 0;

  txt = (char *)data;



  while ((c = fgetc(f_in)) != EOF && c != '\x0a' && c != '\x0d') {

  while ((c = fgetc(f_in)) != EOF && c != '\x0a' && c != '\x0d')

  {

    txt[data_len] = c;

    ++data_len;

    if (allocated - data_len < 1) {      // increase allocated memory

    if (allocated - data_len < 1)

    { // increase allocated memory

      allocated += 16 * 1024;

      data = realloc(data, allocated);

      txt = (char *)data;

    }

  }

  if (data_len == 0 && c == EOF) {

  if (data_len == 0 && c == EOF)

  {

    free(data);

    return 1;

  }
@@ -635,7 +636,8 @@ int read_obj_func_text(FILE *f_in, long int dimensions, P_VOID &data, long int & 
  txt[data_len] = '\0';

  ++data_len;



  if (c == '\x0d') {		// read LF following CR

  if (c == '\x0d')

  { // read LF following CR

    c = fgetc(f_in);

    if (c != '\x0a')

      ungetc(c, f_in);
@@ -653,11 +655,13 @@ int read_obj_func_text(FILE *f_in, long int dimensions, P_VOID &data, long int & 


static int weightInsDelDNA = 3;



void setWeightInsDelDNA(int w) {

void setWeightInsDelDNA(int w)

{

  weightInsDelDNA = w;

}



int getWeightInsDelDNA() {

int getWeightInsDelDNA()

{

  return weightInsDelDNA;

}
@@ -685,41 +689,64 @@ static int changeMatrixDNA[23][23] = { 
    {3, 5, 4, 5, 6, 5, 5, 5, 6, 1, 3, 5, 2, 5, 4, 3, 4, 9, 5, 0, 3, 2, 2},

    {3, 3, 3, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 6, 3, 3, 3, 6, 4, 3, 0, 2, 2},

    {2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2},

	{2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0 }

};

    {2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0}};



inline int getCharMatrixIndexDNA(char chr) {

	switch (chr) {

		case 'A': return 0;

		case 'R': return 1;

		case 'N': return 2;

		case 'D': return 3;

		case 'C': return 4;

		case 'Q': return 5;

		case 'E': return 6;

		case 'G': return 7;

		case 'H': return 8;

		case 'I': return 9;

		case 'L': return 10;

		case 'K': return 11;

		case 'M': return 12;

		case 'F': return 13;

		case 'P': return 14;

		case 'S': return 15;

		case 'T': return 16;

		case 'W': return 17;

		case 'Y': return 18;

		case 'V': return 19;

		case 'X': return 20;

		case 'Z': return 21;

		case 'B': return 22;

inline int getCharMatrixIndexDNA(char chr)

{

  switch (chr)

  {

  case 'A':

    return 0;

  case 'R':

    return 1;

  case 'N':

    return 2;

  case 'D':

    return 3;

  case 'C':

    return 4;

  case 'Q':

    return 5;

  case 'E':

    return 6;

  case 'G':

    return 7;

  case 'H':

    return 8;

  case 'I':

    return 9;

  case 'L':

    return 10;

  case 'K':

    return 11;

  case 'M':

    return 12;

  case 'F':

    return 13;

  case 'P':

    return 14;

  case 'S':

    return 15;

  case 'T':

    return 16;

  case 'W':

    return 17;

  case 'Y':

    return 18;

  case 'V':

    return 19;

  case 'X':

    return 20;

  case 'Z':

    return 21;

  case 'B':

    return 22;

  }

  printf("UNKNOWN LETTER '%c' IN THE DNA SEQUENCE!!! Aborting program.\n", chr);

  exit(-1);

  // return -1;

}





T_DISTANCE dist_func_dna(void *p1, long int p1_len, void *p2, long int p2_len, T_DISTANCE threshold)

{

  int *d;          // pointer to vector
@@ -753,10 +780,12 @@ T_DISTANCE dist_func_dna(void *p1, long int p1_len, void *p2, long int p2_len, T 


  // Step 1



  if (p1_len <= 0) {

  if (p1_len <= 0)

  {

    return p2_len * weightInsDelDNA;

  }

  if (p2_len <= 0) {

  if (p2_len <= 0)

  {

    return p1_len * weightInsDelDNA;

  }

  d = (int *)malloc((p2_len + 1) * sizeof(int));
@@ -769,7 +798,8 @@ T_DISTANCE dist_func_dna(void *p1, long int p1_len, void *p2, long int p2_len, T 
  // Step 3

  s_i = (char *)p1;



  for (i = 1; i <= p1_len; i++) {

  for (i = 1; i <= p1_len; i++)

  {



    d[0] = i * weightInsDelDNA; // Deleting i letters from the first string ???

    diag_prev = (i - 1) * weightInsDelDNA;
@@ -777,7 +807,8 @@ T_DISTANCE dist_func_dna(void *p1, long int p1_len, void *p2, long int p2_len, T 
    // Step 4

    t_j = (char *)p2;



    for (j = 1; j <= p2_len; j++) {

    for (j = 1; j <= p2_len; j++)

    {



      // Step 5