/usr/include/pbseq/alignment/algorithms/anchoring/BasicEndpointImpl.hpp is in libblasr-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 | #ifndef _BLASR_BASIC_ENDPOINT_IMPL_HPP_
#define _BLASR_BASIC_ENDPOINT_IMPL_HPP_
#include "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
|