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/*
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';
}
}
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