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#ifndef _BLASR_TUPLE_COUNT_TABLE_IMPL_HPP_
#define _BLASR_TUPLE_COUNT_TABLE_IMPL_HPP_
#include <pbdata/utils.hpp>
template <typename TSequence, typename TTuple>
void TupleCountTable<TSequence, TTuple>::InitCountTable(TupleMetrics &ptm)
{
Free();
tm = ptm;
tm.InitializeMask();
assert(tm.tupleSize > 0);
// create the mask just in case the ptm is not initialized
// properly.
countTableLength = 4;
countTableLength = countTableLength << ((tm.tupleSize - 1) * 2);
assert(countTableLength > 0);
countTable = ProtectedNew<int>(countTableLength);
deleteStructures = true;
std::fill(&countTable[0], &countTable[countTableLength], 0);
nTuples = 0;
}
template <typename TSequence, typename TTuple>
TupleCountTable<TSequence, TTuple>::TupleCountTable()
{
countTable = NULL;
countTableLength = 0;
nTuples = 0;
deleteStructures = false;
}
template <typename TSequence, typename TTuple>
TupleCountTable<TSequence, TTuple>::~TupleCountTable()
{
Free();
}
template <typename TSequence, typename TTuple>
void TupleCountTable<TSequence, TTuple>::Free()
{
if (deleteStructures == false) {
//
// Do not delete this if it is referencing another structure
//
return;
}
if (countTable != NULL) {
delete[] countTable;
countTable = NULL;
}
countTableLength = nTuples = 0;
}
template <typename TSequence, typename TTuple>
void TupleCountTable<TSequence, TTuple>::IncrementCount(TTuple &tuple)
{
TupleData tupleIndex = TupleData(tuple.tuple);
assert(tupleIndex < countTableLength);
countTable[tupleIndex]++;
++nTuples;
}
template <typename TSequence, typename TTuple>
void TupleCountTable<TSequence, TTuple>::AddSequenceTupleCountsLR(TSequence &seq)
{
VectorIndex i;
TTuple tuple;
if (seq.length >= static_cast<DNALength>(tm.tupleSize)) {
for (i = 0; i < seq.length - tm.tupleSize + 1; i++) {
if (tuple.FromStringLR(&seq.seq[i], tm)) {
IncrementCount(tuple);
}
}
}
}
template <typename TSequence, typename TTuple>
void TupleCountTable<TSequence, TTuple>::Write(std::ofstream &out)
{
out.write((char *)&countTableLength, sizeof(int));
out.write((char *)&nTuples, sizeof(int));
out.write((char *)&tm.tupleSize, sizeof(int));
out.write((char *)countTable, sizeof(int) * countTableLength);
}
template <typename TSequence, typename TTuple>
void TupleCountTable<TSequence, TTuple>::Read(std::ifstream &in)
{
Free(); // Clear before reusing this object.
in.read((char *)&countTableLength, sizeof(int));
in.read((char *)&nTuples, sizeof(int));
in.read((char *)&tm.tupleSize, sizeof(int));
tm.InitializeMask();
countTable = ProtectedNew<int>(countTableLength);
deleteStructures = true;
in.read((char *)countTable, sizeof(int) * countTableLength);
}
#endif
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