/* Aplica una funcion a todos los elementos del árbol */
void map_tree(void (*func)(void *), TREE *t)
{
TREE *c;
if(t->childs != NULL)
{
c = (TREE *)first_l(t->childs);
while(c != NULL)
{
map_tree(func, c);
c = (TREE *)next_l(t->childs);
}
}
(*func)(t->value);
}
/* Libera todo el árbol */
void free_tree(TREE *t)
{
TREE *c;
if(t->childs != NULL)
{
c = (TREE *)first_l(t->childs);
while(c != NULL)
{
free_tree(c);
c = (TREE *)next_l(t->childs);
}
free_l(t->childs);
}
free(t);
}
/*
* refill the msequencecontainer object with the next set of sequences and descriptions
*/
unsigned long msequenceServer::next(const bool _f)
{
/*
* exit on completion
*/
if(done())
return 0;
/*
* start the reading process, if it hasn't been started
*/
if(!started()) {
if(!start()) {
m_bDone = true;
m_bError = true;
m_strStatus += "Server would not start.\r\n";
return 0;
}
}
if(m_lFileType == XBANG)
return next_pro(_f);
if(!_f)
return next_l();
/*
* initialized the time
*/
double dStart = clock();
unsigned long iLength = 0;
msequence seqTemp;
char cValue = '\0';
char *pValue = NULL;
char *pEol = NULL;
m_pCol->clear();
while(!feof(m_pInput) && iLength < m_pCol->m_tMax) {
/*
* store the description in a temporary msequence object, obtained in the previous read
*/
m_pCol->m_vASequences[iLength].m_strDes = m_strFirst;
/*
* strip whitespace characters from the sequence line
*/
pValue = m_pLine;
fgets(pValue,m_lSize,m_pInput);
/*
* clear the sequence in a temporary msequence object
*/
while(pValue[0] != '>' && !feof(m_pInput)) {
/*
* store initial sequence line, and repeat until the next description line is encountered
*/
pValue += strlen(pValue);
pValue--;
if(pValue > m_pLine) {
while(pValue > m_pLine && isspace(*pValue)) {
pValue--;
}
if(!isspace(*pValue) && *pValue != '\0') {
pValue++;
*pValue = '\0';
}
}
fgets(pValue,m_lSize,m_pInput);
}
cValue = *pValue;
*pValue = '\0';
bz(m_pLine);
m_pCol->m_vASequences[iLength].m_strSeq = m_pLine;
m_pCol->m_vASequences[iLength].m_siPath = (short int)(m_vstrPaths.size() - 1);
*pValue = cValue;
/*
* store the next description line
*/
if(pValue[0] == '>') {
if(strchr(pValue,0x01)) {
pEol = strchr(pValue,0x01);
*pEol = '\0';
}
else {
pEol = pValue + strlen(pValue) - 1;
while(pEol > pValue && isspace(*pEol)) {
*pEol = '\0';
pEol--;
}
}
pEol = strchr(pValue,'\r');
if(pEol) {
*pEol = '\0';
}
pEol = strchr(pValue,'\n');
if(pEol) {
*pEol = '\0';
}
m_strFirst = pValue + 1;
}
m_pCol->m_tLength++;
iLength++;
}
/*
* if the current sequence list file is finished, close it and get the next one, otherwise finish
*/
if(feof(m_pInput)) {
if(m_dstrFasta.empty()) {
finish();
}
else {
fclose(m_pInput);
start();
}
}
/*
* store the time required to load the msequencecontainer
*/
m_dTime += (double)(clock() - dStart);
return iLength;
}
