/usr/include/blasr/algorithms/anchoring/BasicEndpoint.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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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 | #ifndef _BLASR_BASIC_ENDPOINT_HPP_
#define _BLASR_BASIC_ENDPOINT_HPP_
#include "Types.h"
#include "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 "algorithms/anchoring/BasicEndpointImpl.hpp"
#endif
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