void clear (u_int64_t toErase)
{
u_int64_t totalPhysical = System::info().getMemoryPhysicalTotal();
if (toErase == 0) { toErase = totalPhysical; }
size_t blockSize = 32*1024;
u_int32_t nbIter = toErase/blockSize;
vector<void*> buffers (nbIter, 0);
SubjectIterator<u_int32_t> it (new Range<u_int32_t>::Iterator (1, nbIter), nbIter/100);
it.addObserver (new ProgressTimer (nbIter, "clear cache"));
size_t i=0;
for (it.first(); !it.isDone(); it.next())
{
void* b = calloc (blockSize, 1);
if (b != 0) { buffers[i]=b; i++; }
}
//#if 0
// size_t j=0;
// for (size_t k=0; k<nbIter; k++)
// {
// void* b = buffers[k];
// if (b != 0) { free (b); j++; }
// }
//#endif
}
int main (int argc, char* argv[])
{
// We declare a STL list with some values.
int values[] = {1,2,3,5,8,13,21,34};
int valuesLen = sizeof(values)/sizeof(values[0]);
std::list<int> l (values, values + valuesLen);
// We create an iterator on the list.
ListIterator<int>* itList = new ListIterator<int> (l);
// We declare an iterator that will send progress status every 3 iterations.
// Note that it refers a ListIterator instance given as constructor parameter.
SubjectIterator<int> itNotif (itList, 3);
// We create some listener to be notified about progress and attach it to the iterator.
itNotif.addObserver (new ProgressFunctor ());
// We iterate the truncated list
for (itNotif.first(); !itNotif.isDone(); itNotif.next())
{
// We can do something in the loop, but there is nothing here about progress management
}
}
int main (int argc, char* argv[])
{
if (argc < 2)
{
std::cerr << "you must provide a bank." << std::endl;
return EXIT_FAILURE;
}
// We define a try/catch block in case some method fails
try
{
// We declare an input Bank and use it locally
IBank* inputBank = Bank::open (argv[1]);
LOCAL (inputBank);
// Note also that we have to parameterize the SubjectIterator by the kind of iterated
// items (Sequence) and the processing that has to be done on each iteration (ProgressFunctor).
SubjectIterator<Sequence> iter (inputBank->iterator(), 10);
// We create some listener to be notified every 10 iterations and attach it to the iterator.
iter.addObserver (new ProgressFunctor());
// We loop over sequences.
for (iter.first(); !iter.isDone(); iter.next())
{
// Note that we do nothing inside the sequence iterating loop about the progression management.
// In other words, we don't "pollute" the code inside this loop by presentation concerns and
// we can therefore focus on the job to be done on the iterated sequences.
}
}
catch (Exception& e)
{
std::cerr << "EXCEPTION: " << e.getMessage() << std::endl;
}
}
void MPHFAlgorithm<span,Abundance_t,NodeState_t>::populate ()
{
size_t nb_iterated = 0;
size_t n = _abundanceMap->size();
_nb_abundances_above_precision = 0;
/** We need a progress object. */
tools::dp::IteratorListener* delegate = createIteratorListener(_solidCounts->getNbItems(),messages[3]); LOCAL (delegate);
setProgress (new ProgressCustom(delegate));
SubjectIterator<Count>* itKmers = new SubjectIterator<Count> (_solidCounts->iterator(), _solidCounts->getNbItems()/100);
itKmers->addObserver (_progress);
LOCAL (itKmers);
// TODO parallize that
std::vector<int> & _abundanceDiscretization = _abundanceMap->_abundanceDiscretization ;
int max_abundance_discrete = _abundanceDiscretization[_abundanceDiscretization.size()-2];
// set counts and at the same time, test the mphf
for (itKmers->first(); !itKmers->isDone(); itKmers->next())
{
//cout << "kmer: " << itKmers->item().value.toString(21) << std::endl;
/** We get the hash code of the current item. */
typename AbundanceMap::Hash::Code h = _abundanceMap->getCode (itKmers->item().value);
/** Little check. */
if (h >= n) { throw Exception ("MPHF check: value out of bounds"); }
/** We get the abundance of the current kmer. */
int abundance = itKmers->item().abundance;
if (abundance > max_abundance_discrete)
{
_nb_abundances_above_precision++;
abundance = max_abundance_discrete;
}
//get first cell strictly greater than abundance
std::vector<int>::iterator up = std::upper_bound(_abundanceDiscretization.begin(), _abundanceDiscretization.end(), abundance);
up--; // get previous cell
int idx = up- _abundanceDiscretization.begin() ;
/** We set the abundance of the current kmer. */
_abundanceMap->at (h) = idx;
nb_iterated ++;
}
if (nb_iterated != n && n > 3)
{
throw Exception ("ERROR during abundance population: itKmers iterated over %d/%d kmers only", nb_iterated, n);
}
#if 1
// you know what? let's always test if the MPHF does not have collisions, it won't hurt.
check ();
#endif
/** We gather some statistics. */
getInfo()->add (1, "stats");
getInfo()->add (2, "nb_keys", "%ld", _abundanceMap->size());
getInfo()->add (2, "data_size", "%ld", _dataSize);
getInfo()->add (2, "bits_per_key", "%.3f", (float)(_dataSize*8)/(float)_abundanceMap->size());
getInfo()->add (2, "prec", "%d", MAX_ABUNDANCE);
getInfo()->add (2, "nb_abund_above_prec", "%d", _nb_abundances_above_precision);
getInfo()->add (1, getTimeInfo().getProperties("time"));
}
