common.c

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/*
 * Commonly used routines.
 *
 * This file is copyright 2002 Jim Kent, but license is hereby
 * granted for all use - public, private or commercial. 
 */


#include "log.h"
#include "linestream.h"
#include "common.h"




/****************************************************************************************
*  Memory functions
****************************************************************************************/



/* 128*8*1024*1024 == 1073741824 == 2^30 on 32 bit machines,size_t == 4 bytes*/
/* on 64 bit machines, size_t = 8 bytes, 2^30 * 2 * 2 = 2^32 == 4 Gb */
static size_t maxAlloc = 128*8*1024*1024*(sizeof(size_t)/4)*(sizeof(size_t)/4);



void *needMem (size_t size)
{
  void *pt;
  pt = hlr_malloc (size);
  memset(pt, 0, size);
  return pt;
}



void *needLargeMem (size_t size)
{
  void *pt;
  pt = hlr_malloc (size);
  return pt;
}



void *needLargeZeroedMem (size_t size)
{
  void *v;
  v = needLargeMem(size);
  memset(v, 0, size);
  return v;
}



void *needLargeMemResize (void* vp, size_t size)
{
  void *pt;
  if (size == 0 || size >= maxAlloc)
    die ("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
         (unsigned long long)size, (unsigned long long)maxAlloc);
  if ((pt = hlr_realloc(vp, size)) == NULL)
    die ("needLargeMemResize: Out of memory - request size %llu bytes\n",
         (unsigned long long)size);
  return pt;
}



void *needLargeZeroedMemResize (void* vp, size_t oldSize, size_t newSize)
{
  void *v = needLargeMemResize(vp, newSize);
  if (newSize > oldSize)
    memset(((char*)v)+oldSize, 0, newSize-oldSize);
  return v;
}



void *cloneMem (void *pt, size_t size)
{
  void *newPt = needLargeMem(size);
  memcpy(newPt, pt, size);
  return newPt;
}



void freeMem (void *pt)
{
  if (pt != NULL) 
    {
      hlr_free(pt);
    }
}



void freez (void *vpt)
{
  void **ppt = (void **)vpt;
  void *pt = *ppt;
  *ppt = NULL;
  freeMem(pt);
}




/****************************************************************************************
* Other Functions
****************************************************************************************/


void zeroBytes (void *vpt, int count)
{
  char *pt = (char*)vpt;
  while (--count>=0)
    *pt++=0;
}



void reverseBytes (char *bytes, long length)
{
  long halfLen = (length>>1);
  char *end = bytes+length;
  char c;
  while (--halfLen >= 0)
    {
      c = *bytes;
      *bytes++ = *--end;
      *end = c;
    }
}



Texta readList (char* fileName)
{
  LineStream ls;
  char *line;
  Texta list;

  list = textCreate (1000);
  ls = ls_createFromFile (fileName);
  while (line = ls_nextLine (ls)) {
    if (line[0] == '\0') {
      continue;
    }
    textAdd (list,line);
  }
  ls_destroy (ls);
  return list;
}




Array readTable (char* fileName, char* delimiter)
{
  Array tableRows;
  TableRow *currTableRow;
  LineStream ls;
  char *line,*token;
  WordIter w;

  tableRows = arrayCreate (1000,TableRow);
  ls = ls_createFromFile (fileName);
  while (line = ls_nextLine (ls)) {
    if (line[0] == '\0') {
      continue;
    }
    currTableRow = arrayp (tableRows,arrayMax (tableRows),TableRow);
    currTableRow->tableColumns = textCreate (10);
    w = wordIterCreate (line,delimiter,0);
    while (token = wordNext (w)) {
      textAdd (currTableRow->tableColumns,token);
    }
    wordIterDestroy (w);
  }
  ls_destroy (ls);
  return tableRows;
}

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