/usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.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 | #ifndef SPARSE_DYNAMIC_PROGRAMMING_H_
#define SPARSE_DYNAMIC_PROGRAMMING_H_
#include <vector>
#include <string>
#include "../../../../pbdata/Types.h"
#include "../../../../pbdata/defs.h"
#include "../../../../pbdata/DNASequence.hpp"
#include "../../../datastructures/alignment/Alignment.hpp"
#include "../AlignmentUtils.hpp"
/*******************************************************************************
* Sparse dynamic programming implementation of Longest Common Subsequence
*
* Implementation of method described in Baker and Giancarlo, Journal of
* Algorithms 42, 231-254, 2002.
*
* 5/7/09 -- Modified to incorporate different linear cost functions, and
* local alignments.
*
******************************************************************************/
int IndelPenalty(int x1, int y1, int x2, int y2, int insertion, int deletion);
template<typename T_Fragment>
void StoreAbove(std::vector<T_Fragment> &fragmentSet, DNALength fragmentLength);
template<typename T_Fragment>
int SDPLongestCommonSubsequence(DNALength queryLength,
std::vector<T_Fragment> &fragmentSet,
DNALength fragmentLength,
int insertion, int deletion, int match,
std::vector<int> &maxFragmentChain, AlignmentType alignType=Global);
#include "SparseDynamicProgrammingImpl.hpp"
#endif
|