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#ifndef _BLASR_BASIC_ENDPOINT_IMPL_HPP_
#define _BLASR_BASIC_ENDPOINT_IMPL_HPP_
#include <alignment/algorithms/anchoring/BasicEndpoint.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.
*/
template <typename T_ScoredFragment>
BasicEndpoint<T_ScoredFragment>::BasicEndpoint()
{
}
template <typename T_ScoredFragment>
WhichEnd BasicEndpoint<T_ScoredFragment>::GetSide()
{
return side;
}
template <typename T_ScoredFragment>
void BasicEndpoint<T_ScoredFragment>::FragmentPtrToStart(T_ScoredFragment *fragment)
{
p.SetX(fragment->GetX());
p.SetY(fragment->GetY());
side = Start;
fragmentPtr = fragment;
}
template <typename T_ScoredFragment>
void BasicEndpoint<T_ScoredFragment>::FragmentPtrToEnd(T_ScoredFragment *fragment)
{
p.SetX(fragment->GetX() + fragment->GetLength());
p.SetY(fragment->GetY() + fragment->GetLength());
side = End;
fragmentPtr = fragment;
}
template <typename T_ScoredFragment>
int BasicEndpoint<T_ScoredFragment>::GetScore()
{
return fragmentPtr->GetScore();
}
template <typename T_ScoredFragment>
int BasicEndpoint<T_ScoredFragment>::SetScore(int score)
{
return (fragmentPtr->SetScore(score));
}
template <typename T_ScoredFragment>
T_ScoredFragment *BasicEndpoint<T_ScoredFragment>::SetScoredReference(
T_ScoredFragment *_fragmentPtr)
{
return (fragmentPtr = _fragmentPtr);
}
template <typename T_ScoredFragment>
int BasicEndpoint<T_ScoredFragment>::operator<(const BasicEndpoint &rhs) const
{
return p < rhs.p;
}
template <typename T_ScoredFragment>
KeyType BasicEndpoint<T_ScoredFragment>::GetKey()
{
return p.GetY();
}
template <typename T_ScoredFragment>
T_ScoredFragment *BasicEndpoint<T_ScoredFragment>::GetFragmentPtr()
{
return fragmentPtr;
}
template <typename T_ScoredFragment>
void BasicEndpoint<T_ScoredFragment>::SetChainPrev(T_ScoredFragment *prevChainFragment)
{
fragmentPtr->SetChainPrev(prevChainFragment);
}
#endif
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