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#ifndef _BLASR_BASIC_ENDPOINT_HPP_
#define _BLASR_BASIC_ENDPOINT_HPP_
#include <pbdata/Types.h>
#include <alignment/algorithms/anchoring/Coordinate.hpp>
//
// An endpoint is one of the ends of a fragment, where
// a fragment is an exact match between two genomes.
// So, a fragment is a 2D object that has a position and length,
// and an endpoint is 1D, where it just has a position.
// A fragment may be associated with a score that is the score
// of the fragment in a maximum scoring chain. When finding a
// maximum scoring chain using priority search trees, one must
// be able to set the score of a fragment when indexing solely
// a point.
//
enum WhichEnd
{
Start,
End
};
typedef UInt KeyType;
template <typename T_ScoredFragment>
class BasicEndpoint
{
private:
Coordinate p;
WhichEnd side;
T_ScoredFragment* fragmentPtr;
public:
class LessThan
{
public:
int operator()(const BasicEndpoint<T_ScoredFragment>& lhs,
const BasicEndpoint<T_ScoredFragment>& rhs) const
{
return lhs.p < rhs.p;
}
};
BasicEndpoint();
WhichEnd GetSide();
void FragmentPtrToStart(T_ScoredFragment* fragment);
void FragmentPtrToEnd(T_ScoredFragment* fragment);
int GetScore();
int SetScore(int score);
T_ScoredFragment* SetScoredReference(T_ScoredFragment* _fragmentPtr);
int operator<(const BasicEndpoint& rhs) const;
KeyType GetKey();
T_ScoredFragment* GetFragmentPtr();
void SetChainPrev(T_ScoredFragment* prevChainFragment);
};
#include "BasicEndpointImpl.hpp"
#endif
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