16ssearcher.hh

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#pragma once
#include <string>
#include <stdint.h>
#include <vector>
#include <map>

struct Entry16S
{
  uint32_t id;
  int hits;
};

class Search16S
{
public:
  Search16S(const std::string& src, int indexLength);
  void score(const std::string& nucleotides);
  std::vector<Entry16S> topScores();
  void printTop(unsigned int top);
private:
  typedef std::map<uint32_t, std::vector<unsigned int> > hashes_t;
  hashes_t d_hashes;
  std::vector<Entry16S> d_entries;
};