double CRateMonitor::GetRate(void) const
{
if (m_Rate > 0.0)
return m_Rate;
size_t n = m_Data.size();
if (n < 2)
return GetPace();
list<TMark> gaps;
if (n > 2) {
TMark prev = m_Data.front();
list<TMark>::const_iterator it = m_Data.begin();
_ASSERT(prev.first - m_Data.back().first > kSpan);
for (++it; it != m_Data.end(); ++it) {
TMark next = *it;
double dt = prev.second - next.second;
if (dt < kSpan) {
#ifdef DEBUG_RATE_MONITOR
cout << "dt = " << dt << ",\td =" << (kSpan - dt)
<< ",\tn = " << distance(m_Data.begin(), it) << endl;
#endif //DEBUG_RATE_MONITOR
_DEBUG_ARG(list<TMark>::const_iterator beg = m_Data.begin());
_ASSERT(it == ++beg);
continue;
}
gaps.push_back(make_pair(prev.first - next.first, dt));
prev = next;
}
} else {
double dt = m_Data.front().second - m_Data.back().second;
if (dt < kSpan)
return GetPace();
gaps.push_back(make_pair(m_Data.front().first -
m_Data.back ().first, dt));
}
_ASSERT(!gaps.empty() && !m_Rate);
double weight = 1.0;
for (;;) {
double rate = gaps.front().first / gaps.front().second;
gaps.pop_front();
if (gaps.empty()) {
m_Rate += rate * weight;
break;
}
double w = weight * kWeight;
m_Rate += rate * w;
weight -= w;
}
return m_Rate;
}
Uint4
SplitQuery_CalculateNumChunks(EBlastProgramType program,
size_t *chunk_size,
size_t concatenated_query_length,
size_t num_queries)
{
if ( !SplitQuery_ShouldSplit(program, *chunk_size,
concatenated_query_length, num_queries)) {
_TRACE("Not splitting queries");
return 1;
}
size_t overlap_size = SplitQuery_GetOverlapChunkSize(program);
Uint4 num_chunks = 0;
_DEBUG_ARG(size_t target_chunk_size = *chunk_size);
// For translated queries the chunk size should be divisible by CODON_LENGTH
if (Blast_QueryIsTranslated(program)) {
size_t chunk_size_delta = ((*chunk_size) % CODON_LENGTH);
*chunk_size -= chunk_size_delta;
_ASSERT((*chunk_size % CODON_LENGTH) == 0);
}
// Fix for small query size
if ((*chunk_size) > overlap_size) {
num_chunks = concatenated_query_length / ((*chunk_size) - overlap_size);
}
// Only one chunk, just return;
if (num_chunks <= 1) {
*chunk_size = concatenated_query_length;
return 1;
}
// Re-adjust the chunk_size to make load even
if (!Blast_QueryIsTranslated(program)) {
*chunk_size = (concatenated_query_length + (num_chunks - 1) * overlap_size) / num_chunks;
// Round up only if this will not decrease the number of chunks
if (num_chunks < (*chunk_size) - overlap_size ) (*chunk_size)++;
}
_TRACE("Number of chunks: " << num_chunks << "; "
"Target chunk size: " << target_chunk_size << "; "
"Returned chunk size: " << *chunk_size);
return num_chunks;
}
