https://github.com/sanger-pathogens/gubbins
Tip revision: afc51e6c7b0dcdb43842b4db5aaf6f799f5f7c3c authored by Christoph PĆ¼the on 20 January 2020, 10:25:33 UTC
Merge pull request #271 from sanger-pathogens/gdb
Merge pull request #271 from sanger-pathogens/gdb
Tip revision: afc51e6
seqUtil.c
#define __SEQUTIL_C__
#include "seqUtil.h"
#include "string_cat.h"
/*
* Yu-Wei Wu http://yuweibioinfo.blogspot.com/2008/10/newick-tree-parser-in-c-make-use-of.html
* Copyright (C) 2011 Yu-Wei Wu
*
* This program 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.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
typedef struct seqMem
{
void *pos;
struct seqMem *next;
} seqMem;
seqMem *start;
seqMem *current;
void seqMemInit()
{
start = NULL;
}
void* seqMalloc(int size)
{
if (start == NULL)
{
start = malloc(sizeof(seqMem));
memset(start, '\0', sizeof(seqMem));
current = start;
}
else
{
current->next = malloc(sizeof(seqMem));
memset(current->next, '\0', sizeof(seqMem));
current = current->next;
}
current->pos = malloc(size);
memset(current->pos, '\0', size);
return(current->pos);
}
void seqFreeAll()
{
while (start != NULL)
{
current = start->next;
free(start->pos);
free(start);
start = current;
}
start = NULL;
}
void seqFree(void* pos)
{
seqMem *node, *prenode;
node = start;
prenode = start;
while (node != NULL)
{
if (node->pos == pos)
{
free(node->pos);
if (node == start)
{
start = node->next;
}
else if (node->next == NULL)
{
current = prenode;
prenode->next = NULL;
}
else
{
prenode->next = node->next;
}
free(node);
break;
}
prenode = node;
node = node->next;
}
}
void inputString(char *input, char **ppcStr, int *iLen, int *iMaxLen)
{
int inputLen;
char *temp;
inputLen = size_of_string(input);
if (inputLen == 0)
{
return;
}
while (*iMaxLen < (*iLen + inputLen) + 1)
{
*iMaxLen = *iMaxLen + APPEND_LEN;
}
temp = seqMalloc(*iMaxLen);
if (*ppcStr == NULL)
{
memcpy(temp, input, inputLen);
}
else
{
memcpy(temp, *ppcStr, *iLen);
strcat(temp, input);
}
*iLen = *iLen + inputLen;
if (*ppcStr != NULL)
{
seqFree(*ppcStr);
}
*ppcStr = temp;
}