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#ifndef _BLASR_HASHED_TUPLE_LIST_HPP_
#define _BLASR_HASHED_TUPLE_LIST_HPP_
#include <alignment/tuples/TupleList.hpp>
#include <alignment/tuples/TupleMetrics.hpp>
#include <pbdata/DNASequence.hpp>
template <typename T_Tuple>
class HashedTupleList
{
public:
long mask;
std::vector<TupleList<T_Tuple> > hashTable;
int hashLength;
int hashTableLength;
typedef T_Tuple Tuple;
//
// Provide a default constructor with a small
// tuple size for testing.
//
HashedTupleList();
void Initialize(int _hashLength);
HashedTupleList(int _hashLength);
void clear();
void Clear();
void Sort();
void Append(T_Tuple tuple);
void Insert(T_Tuple tuple);
int Find(T_Tuple tuple);
void Print();
//
// Provide a version of find that stores easy access to
// the original tuple.
//
int Find(T_Tuple tuple, int &hashValue, int &index);
void FindAll(T_Tuple &tuple, typename std::vector<T_Tuple>::const_iterator &firstPos,
typename std::vector<T_Tuple>::const_iterator &endPos);
int GetHashLength();
};
template <typename T_Tuple>
void SequenceToHash(DNASequence &seq, HashedTupleList<T_Tuple> &hash, TupleMetrics &tm);
#include "HashedTupleList.hpp"
#endif
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