void SAReader::readElems(SAElemVector& elemVector)
{
assert(m_stage == SAIOS_ELEM);
size_t cap = elemVector.capacity();
size_t num_read = 0;
SAElem e;
while(*m_pReader >> e)
{
elemVector.push_back(e);
++num_read;
}
assert(cap >= num_read);
(void)cap;
m_stage = SAIOS_DONE;
}
void SuffixArray::removeReads(const NumericIDSet& idSet)
{
// Early exit if the idset is empty
if(idSet.empty())
return;
SAElemVector newData;
newData.reserve(m_data.size());
for(size_t idx = 0; idx < m_data.size(); ++idx)
{
SAElem id = m_data[idx];
if(idSet.find(id.getID()) == idSet.end())
{
// not on the delete list
newData.push_back(id);
}
}
m_data.swap(newData);
m_numStrings -= idSet.size();
}
