SENNA_Hash.c

#include "SENNA_utils.h"
#include "SENNA_Hash.h"

#define MAX_KEY_SIZE 256

SENNA_Hash* SENNA_Hash_new(const char *path, const char *filename)
{
  FILE *f;
  SENNA_Hash *hash;
  char **keys = NULL;
  int n_keys;
  char key[MAX_KEY_SIZE];		//@AureDi temporary array of key, which stores the characters from filenames.
  int i;

  SENNA_message("loading hash: %s%s", (path ? path : ""), (filename ? filename : ""));

  //@AureDi Count the number of  key (maximum is 256 characters)
  f = SENNA_fopen(path, filename, "rt"); /* the t is to comply with Windows */
  n_keys = 0;
  while(fgets(key, MAX_KEY_SIZE, f))
    n_keys++;			//@AureDi Remember reading how many times
  SENNA_fclose(f);
  keys = SENNA_malloc(n_keys, sizeof(char*));	//@AureDi 

  f = SENNA_fopen(path, filename, "rt"); /* the t is to comply with Windows */
  n_keys = 0;
  while(fgets(key, MAX_KEY_SIZE, f))
  {
    int key_size = strlen(key);
	//@ We can assume that the length of each line is not exceeded 255.
    key[key_size-1] = '\0'; /* discard the newline */	//@AureDi \0 is the sign of the end. Because this method is applied to process single word, so we can assume the end word is newline character .
    keys[n_keys] = SENNA_malloc(key_size, sizeof(char));
    strcpy(keys[n_keys], key);
    n_keys++;
  }
  SENNA_fclose(f);

  hash = SENNA_malloc(sizeof(SENNA_Hash), 1);
  hash->keys = keys;	//@AureDi keys is the pointer of second array.
  hash->size = n_keys;	//@AureDi n_keys is the length of second aaay
  hash->is_admissible_key = NULL;	//@AUreDi admissible

  /* sorted or unsorted hash ? */
  /* (unsorted cannot return an index for a key) */
  hash->is_sorted = 1;		// uper is roght
  for(i = 0; i < n_keys-1; i++)
  {
    if(strcmp(keys[i], keys[i+1]) >= 0)
    {
      hash->is_sorted = 0;
      break;
    }
  }

  return hash;
}

SENNA_Hash *SENNA_Hash_new_with_admissible_keys(const char *path, const char *filename, const char *admissible_keys_filename)
{
  SENNA_Hash *hash = SENNA_Hash_new(path, filename);
  FILE *f;
  int admissiblekeyssize = 0;

  f = SENNA_fopen(path, admissible_keys_filename, "rb");	//@Aure b means that the file is binary file.
  SENNA_fseek(f, 0, SEEK_END);		//@Aure   #define SEEK_END    2    Reposition stream position indicator
  admissiblekeyssize = SENNA_ftell(f);	//@  Get current position in stream

  if(admissiblekeyssize != hash->size)
    SENNA_error("inconsistent hash and admissible key files");

  SENNA_fseek(f, 0, SEEK_SET);
  hash->is_admissible_key = SENNA_malloc(sizeof(char), admissiblekeyssize);
  SENNA_fread(hash->is_admissible_key, 1, admissiblekeyssize, f);		//@ Read block of data from stream to char array is_admissible_key.
  SENNA_fclose(f);

  return hash;
}

void SENNA_Hash_convert_IOBES_to_IOB(SENNA_Hash *hash)
{
  int i;

  for(i = 0; i < hash->size; i++)
  {
    char *key = hash->keys[i];
    if(strlen(key) < 3)	//@ The length of ES is exceeded 2. 
      continue;

    if( (key[0] == 'E') && (key[1] == '-') )
      key[0] = 'I';

    if( (key[0] == 'S') && (key[1] == '-') )
      key[0] = 'B';
  }
}

void SENNA_Hash_convert_IOBES_to_brackets(SENNA_Hash *hash)
{
  int i, j;
  
  for(i = 0; i < hash->size; i++)
  {
    char *key = hash->keys[i];
    int key_size = strlen(key);

    if(!strcmp(key, "O"))
      key[0] = '*';

    if(key_size < 3)
      continue;

    if( (key[0] == 'B') && (key[1] == '-') )
    {
      key[0] = '(';
      for(j = 1; j < key_size-1; j++)
        key[j] = key[j+1];
      key[key_size-1] = '*';
    }

    if( (key[0] == 'I') && (key[1] == '-') )
    {
      key[0] = '*';
      key[1] = '\0';
    }

    if( (key[0] == 'E') && (key[1] == '-') )
    {
      key[0] = '*';
      key[1] = ')';
      key[2] = '\0';
    }

    if( (key[0] == 'S') && (key[1] == '-') )
    {
      key = SENNA_realloc(key, key_size+2, sizeof(char));
      
      key[0] = '(';
      for(j = 1; j < key_size-1; j++)
        key[j] = key[j+1];
      key[key_size-1] = '*';
      key[key_size] = ')';
      key[key_size+1] = '\0';

      hash->keys[i] = key;
    }
  }
}

void SENNA_Hash_free(SENNA_Hash *hash)
{
  int i;

  for(i = 0; i < hash->size; i++)
    SENNA_free(hash->keys[i]);
  SENNA_free(hash->keys);
  if(hash->is_admissible_key)
    SENNA_free(hash->is_admissible_key);
  SENNA_free(hash);
}

int SENNA_Hash_index(SENNA_Hash *hash, const char *key)
{
  char **keys = hash->keys;
  int idxinf = 0;
  int idxsup = hash->size-1;

  if(!hash->is_sorted)
    SENNA_error("cannot search a key into an unsorted hash");

  if(strcmp(key, keys[idxinf]) < 0 || strcmp(key, keys[idxsup]) > 0)
    return -1;

  while(idxinf <= idxsup)
  {
    int idxmiddle = (idxsup+idxinf)/2;
    int status = strcmp(key, keys[idxmiddle]);
/*    printf("%d %d %d [%d]\n", idxinf, idxmiddle, idxsup, status); */
    if(status < 0)
      idxsup = idxmiddle-1;
    else if(status > 0)
      idxinf = idxmiddle+1;
    else
      return idxmiddle;
  }

  return -1;
}

const char* SENNA_Hash_key(SENNA_Hash *hash, int idx)
{
  if( (idx < 0) || (idx >= hash->size) )
    SENNA_error("hash index out of bounds");

  return hash->keys[idx];
}

int SENNA_Hash_size(SENNA_Hash *hash)
{
  return hash->size;
}

char SENNA_Hash_is_admissible_index(SENNA_Hash *hash, int idx)
{
  if(!hash->is_admissible_key)
    SENNA_error("hash does not handle admissible keys");

  if( (idx < 0) || (idx >= hash->size) )
    SENNA_error("hash index out of bounds");

  return hash->is_admissible_key[idx];
}