/usr/include/blasr/algorithms/sorting/LightweightSuffixArray.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 | #ifndef ALGORITHMS_SORTING_LIGHTWEIGHT_SUFFIX_ARRAY_H_
#define ALGORITHMS_SORTING_LIGHTWEIGHT_SUFFIX_ARRAY_H_
#include <algorithm>
#include "qsufsort.hpp"
#include "MultikeyQuicksort.hpp"
#include "DifferenceCovers.hpp"
#include "Types.h"
/*
* a - b potentially may not fit into a signed type. Use some logic
* to get around that.
*/
UInt DiffMod(UInt a, UInt b, UInt d);
void BuildDiffCoverReverseLookup(UInt diffCover[], UInt diffCoverLength,
UInt reverseDiffCover[] // of size diffCoverSize
);
UInt DiffCoverFindH(UInt diffCover[], UInt diffCoverLength, UInt diffCoverSize, UInt textSize);
class DiffCoverMu {
public:
UInt *diffCoverReverseLookup;
UInt diffCoverLength;
UInt diffCoverSize;
UInt textSize;
UInt h;
UInt *diffCover;
UInt compute(UInt i, UInt j);
UInt operator()(const UInt k);
DiffCoverMu();
~DiffCoverMu();
void Initialize(UInt diffCoverP[], UInt diffCoverLengthP, UInt diffCoverSizeP, UInt textSizeP);
};
void BuildDiffCoverLookup(UInt diffCover[], UInt diffCoverLength, UInt v, UInt diffCoverLookup[]);
class DiffCoverDelta {
public:
UInt *diffCoverLookup;
UInt diffCoverSize;
void Initialize(UInt diffCoverP[], UInt diffCoverLengthP, UInt diffCoverSizeP);
UInt operator()(UInt i, UInt j);
~DiffCoverDelta();
};
UInt NCompareSuffices(unsigned char text[], UInt a, UInt b, UInt n);
UInt ComputeDSetSize(UInt diffCover, UInt diffCoverLength, UInt diffCoverSize, UInt textSize);
void ComputeSufVNaming(UInt diffCover[], UInt diffCoverLength, UInt diffCoverN, UInt textSize, UInt lexNaming[],
DiffCoverMu &mu,
UInt sufVNaming[]);
UInt IndexToDiffCoverIndex(UInt index, UInt diffCoverlookup[], UInt diffCoverSize, UInt diffCoverLength );
void DiffCoverComputeLOrder(UInt sufVNaming[], UInt sufVNamingLength, UInt maxVNaming, UInt textLength, DiffCoverMu &mu, UInt lOrder[]);
/*
* Build the lex naming of the v-ordered suffices.
*
* Input: textVOrder - the v-ordering of a subset of the text.
* textSize - the size of the v-order set.
* diffCover - the diff cover used, and it's length
* diffCoverLength
* diffCoverSize - the size of the diff cover.
* Output: lexNaming: the lex-naming of the v-order suffices. The
* names are implemented as unsigned integers.
* Returns: the largest value of the lex-ordering.
*/
UInt DiffCoverBuildLexNaming( unsigned char text[], UInt textSize,
UInt textVOrder[],
UInt dSetSize, UInt diffCover[], UInt diffCoverLength, UInt diffCoverSize,
UInt diffCoverLookup[],
UInt lexNaming[]);
class DiffCoverCompareSuffices {
public:
UInt *lOrder;
DiffCoverDelta *delta;
UInt diffCoverSize;
UInt diffCoverLength;
UInt *diffCoverReverseLookup;
int operator()(UInt a, UInt b);
};
bool LightweightSuffixSort(unsigned char text[], UInt textLength, UInt *index, int diffCoverSize);
#endif
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