/usr/include/pbseq/alignment/tuples/HashedTupleList.hpp is in libblasr-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | #ifndef _BLASR_HASHED_TUPLE_LIST_HPP_
#define _BLASR_HASHED_TUPLE_LIST_HPP_
#include "TupleList.hpp"
#include "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 "tuples/HashedTupleList.hpp"
#endif
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