utility.c

/*
Copyright 2009 John Marshall (jm18@sanger.ac.uk) 

    This file is part of Velvet.

    Velvet is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    Velvet is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with Velvet; if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA

*/
#include <string.h>
#include <stdlib.h>
#include <stdarg.h>
#include <stdio.h>
#include <errno.h>
#include <sys/time.h>

#include "globals.h"
#include "utility.h"

static void allocExitError(const char *function, unsigned long long count,
                          unsigned long long size, const char *name)
{
       if (size == 1)
               exitErrorf(EXIT_FAILURE, true,
                          "Can't %s %llu %ss",
                          function, count, name);
       else
               exitErrorf(EXIT_FAILURE, true,
                          "Can't %s %llu %ss totalling %llu bytes",
                          function, count, name, count * size);
}

void *mallocOrExit3(size_t count, size_t size, const char *name)
{
       void *p = malloc(count * size);
       if (p == NULL && count > 0)
               allocExitError("malloc", count, size, name);

       return p;
}

void *callocOrExit3(size_t count, size_t size, const char *name)
{
       void *p = calloc(count, size);
       if (p == NULL && count > 0)
               allocExitError("calloc", count, size, name);

       return p;
}

void *reallocOrExit4(void *ptr, size_t count, size_t size, const char *name)
{
       void *p = realloc(ptr, count * size);
       if (p == NULL && count > 0)
               allocExitError("realloc", count, size, name);

       return p;
}


static const char *programName = NULL;

void setProgramName(const char *name)
{
       programName = name;
}

void exitErrorf(int exitStatus, boolean showErrno, const char *format, ...)
{
       int savedErrno = errno;
       va_list args;
       va_start(args, format);
       if (programName)
               fprintf(stderr, "%s: ", programName);
       vfprintf(stderr, format, args);
       if (showErrno)
               fprintf(stderr, ": %s", strerror(savedErrno));
       fprintf(stderr, "\n");
       va_end(args);

#ifdef DEBUG 
	abort();
#endif 
       exit(exitStatus);
}

void velvetLog(const char *format, ...)
{
  static boolean timeIsSet = false;
  static struct timeval tvStart;
  struct timeval tvNow;
  struct timeval tvDiff;
  va_list args;

  if (!timeIsSet)
  {
    gettimeofday(&tvStart, NULL);
    timeIsSet = true;
  }

  gettimeofday(&tvNow, NULL);
  timersub(&tvNow, &tvStart, &tvDiff);

  printf("[%ld.%06ld] ", (long) tvDiff.tv_sec, (long) tvDiff.tv_usec);
  va_start(args, format);
  vprintf(format, args);
  va_end(args);

#ifdef DEBUG 
  fflush(stdout);
#endif
}

void velvetFprintf(FILE * file, const char * format, ...) 
{
	va_list args;

	va_start(args, format);
	if (vfprintf(file, format, args) < 0) {
		if (programName)
		       fprintf(stderr, "%s: ", programName);
		fprintf(stderr, "Could not write into file\n");
		va_end(args);
#ifdef DEBUG 
		abort();
#endif 
		exit(EXIT_FAILURE);
	}
	va_end(args);
}

StringBuffer *newStringBuffer(size_t size)
{
	StringBuffer *buffer;

	buffer = callocOrExit(1, StringBuffer);
	if (size > 0)
	{
		buffer->str = callocOrExit(size, char);
		buffer->allocated = size;
	}
	buffer->length = 1; /* virtual count for the final '\0' */

	return buffer;
}

void destroyStringBuffer(StringBuffer *buffer, boolean freeString)
{
	if (!buffer)
		return;

	if (freeString && buffer->allocated > 0)
		free(buffer->str);
	free(buffer);
}

void appendStringBuffer(StringBuffer *buffer, char *str)
{
	int strSize;
	int newSize;

	if (!buffer)
		return;

	strSize = strlen(str);
	newSize = buffer->allocated;

	while (strSize + buffer->length > newSize)
		newSize *= 2;
	if (newSize != buffer->allocated)
	{
		buffer->str = reallocOrExit(buffer->str, newSize, char);
		if (!buffer->allocated)
			*buffer->str = '\0';
		buffer->allocated = newSize;
	}
	buffer->length += strSize;
	buffer->str = strcat(buffer->str, str);
}

void resetStringBuffer(StringBuffer *buffer)
{
	if (buffer && buffer->allocated > 0)
	{
		buffer->length = 1; /* Virtual count for the final '\0' */
		*buffer->str = '\0';
	}
}