StackSeedDomain.h

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#ifndef INTARNA_STACKSEEDDOMAIN_H_
#define INTARNA_STACKSEEDDOMAIN_H_
 
#include "IntaRNA/Interaction.h"
#include "IntaRNA/SeedHandler.h"
#include <functional>
#include <unordered_map>
#include <vector>
 
namespace IntaRNA {
class StackSeedDomain {
public:
    struct Occurrence { size_t i, j, length; };
    StackSeedDomain(const SeedHandler & handler, size_t n, size_t m, size_t span1, size_t span2);
    StackSeedDomain(const std::vector<Occurrence> & occurrences, size_t n, size_t m, size_t span1, size_t span2);
    size_t seedLength(size_t i, size_t j) const;
    size_t seedEndingLength(size_t i, size_t j) const;
    size_t maxSeedLength() const;
    std::vector<Occurrence> minimalOccurrences() const;
    void forEachStart(const std::function<void(size_t,size_t)> & visit) const;
private:
    std::unordered_map<Interaction::BasePair, size_t, Interaction::BasePair::Hash> lengths;
    std::unordered_map<Interaction::BasePair, size_t, Interaction::BasePair::Hash> endingLengths;
    struct Box { size_t i0, i1, j0, j1; };
    std::vector<Box> boxes;
    size_t maximum = 0;
    void add(Occurrence seed, size_t n, size_t m, size_t span1, size_t span2);
};
inline size_t StackSeedDomain::seedLength(size_t i, size_t j) const {
    auto p=lengths.find({i,j}); return p==lengths.end()?0:p->second;
}
inline size_t StackSeedDomain::seedEndingLength(size_t i, size_t j) const {
    auto p=endingLengths.find({i,j}); return p==endingLengths.end()?0:p->second;
}
inline size_t StackSeedDomain::maxSeedLength() const { return maximum; }
}
#endif