/usr/include/libMUSCLE-3.7/libMUSCLE/profile.h is in libmuscle-3.7-dev 3.7+4565-1.
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 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 | #ifndef FastProf2_h
#define FastProf2_h
#include "libMUSCLE/msa.h"
#include "libMUSCLE/pwpath.h"
#include <math.h> // for log function
#include "libMUSCLE/threadstorage.h"
namespace muscle {
class DiagList;
class WeightList;
struct ProfPos
{
bool m_bAllGaps;
unsigned m_uSortOrder[21];
FCOUNT m_fcCounts[20];
FCOUNT m_LL;
FCOUNT m_LG;
FCOUNT m_GL;
FCOUNT m_GG;
SCORE m_AAScores[20];
unsigned m_uResidueGroup;
FCOUNT m_fOcc;
FCOUNT m_fcStartOcc;
FCOUNT m_fcEndOcc;
SCORE m_scoreGapOpen;
SCORE m_scoreGapClose;
#if DOUBLE_AFFINE
SCORE m_scoreGapOpen2;
SCORE m_scoreGapClose2;
#endif
// SCORE m_scoreGapExtend;
};
struct ProgNode
{
ProgNode()
{
m_Prof = 0;
m_EstringL = 0;
m_EstringR = 0;
}
MSA m_MSA;
ProfPos *m_Prof;
PWPath m_Path;
short *m_EstringL;
short *m_EstringR;
unsigned m_uLength;
WEIGHT m_Weight;
};
extern unsigned ResidueGroup[];
const unsigned RESIDUE_GROUP_MULTIPLE = (unsigned) ~0;
extern TLS<PTR_SCOREMATRIX> g_ptrScoreMatrix;
ProfPos *ProfileFromMSA(const MSA &a);
SCORE TraceBack(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, const SCORE *DPM_, const SCORE *DPD_, const SCORE *DPI_,
PWPath &Path);
SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path);
void ProgressiveAlign(const SeqVect &v, const Tree &tree, MSA &a);
SCORE MSAPairSP(const MSA &msa1, const MSA &msa2);
void AlignTwoMSAsGivenPath(const PWPath &Path, const MSA &msaA, const MSA &msaB,
MSA &msaCombined);
void ListProfile(const ProfPos *Prof, unsigned uLength, const MSA *ptrMSA = 0);
SCORE ScoreProfPos2(const ProfPos &PPA, const ProfPos &PPB);
SCORE FastScorePath2(const ProfPos *PA, unsigned uLengthA,
const ProfPos *PB, unsigned uLengthB, const PWPath &Path);
bool IsHydrophilic(const FCOUNT fcCounts[]);
int PAM200_Letter(unsigned uLetter1, unsigned uLetter2);
SCORE AverageMatchScore(const PWPath &Path, unsigned uEdgeIndex,
unsigned uWindowLength);
void WindowSmooth(const SCORE Score[], unsigned uCount, unsigned uWindowLength,
SCORE SmoothScore[], double dCeil = 9e29);
SCORE FastScoreMSA_LA(const MSA &msa, SCORE MatchScore[] = 0);
SCORE FastScoreMSA_NS(const MSA &msa, SCORE MatchScore[] = 0);
SCORE FastScoreMSA_SP(const MSA &msa, SCORE MatchScore[] = 0);
bool RefineMSA(MSA &msa, const Tree &tree);
SCORE MSAQScore(const MSA &msa, SCORE MatchScore[] = 0);
bool RefineBiParts(MSA &msa, const Tree &tree, bool R);
void FindAnchorCols(const MSA &msa, unsigned AnchorCols[],
unsigned *ptruAnchorColCount);
double PctIdToHeight(double dPctId);
double PctIdToHeightKimura(double dPctId);
double PctIdToHeightMAFFT(double dPctId);
double PctIdToMAFFTDist(double dPctId);
bool RefineBlocks(MSA &msa, const Tree &tree);
bool RefineSubfams(MSA &msaIn, const Tree &tree, unsigned uIters);
void SetMuscleTree(const Tree &tree);
void CalcClustalWWeights(const Tree &tree, WEIGHT Weights[]);
void RealignDiffs(const MSA &msaIn, const Tree &Diffs,
const unsigned IdToDiffsTreeNodeIndex[], MSA &msaOut);
void RealignDiffsE(const MSA &msaIn, const SeqVect &v,
const Tree &NewTree, const Tree &OldTree,
const unsigned uNewNodeIndexToOldNodeIndex[],
MSA &msaOut, ProgNode *OldProgNodes);
void RefineTree(MSA &msa, Tree &tree);
void RefineTreeE(MSA &msa, const SeqVect &v, Tree &tree, ProgNode *ProgNodes);
bool IsHydrophobic(const FCOUNT fcCounts[]);
void Hydro(ProfPos *Prof, unsigned uLength);
void SetTermGaps(const ProfPos *Prof, unsigned uLength);
// Macros to simulate 2D matrices
#define DPL(PLA, PLB) DPL_[(PLB)*uPrefixCountA + (PLA)]
#define DPM(PLA, PLB) DPM_[(PLB)*uPrefixCountA + (PLA)]
#define DPD(PLA, PLB) DPD_[(PLB)*uPrefixCountA + (PLA)]
#define DPE(PLA, PLB) DPE_[(PLB)*uPrefixCountA + (PLA)]
#define DPI(PLA, PLB) DPI_[(PLB)*uPrefixCountA + (PLA)]
#define DPJ(PLA, PLB) DPJ_[(PLB)*uPrefixCountA + (PLA)]
#define DPU(PLA, PLB) DPU_[(PLB)*uPrefixCountA + (PLA)]
#define TBM(PLA, PLB) TBM_[(PLB)*uPrefixCountA + (PLA)]
#define TBD(PLA, PLB) TBD_[(PLB)*uPrefixCountA + (PLA)]
#define TBE(PLA, PLB) TBE_[(PLB)*uPrefixCountA + (PLA)]
#define TBI(PLA, PLB) TBI_[(PLB)*uPrefixCountA + (PLA)]
#define TBJ(PLA, PLB) TBJ_[(PLB)*uPrefixCountA + (PLA)]
SCORE ScoreProfPos2LA(const ProfPos &PPA, const ProfPos &PPB);
SCORE ScoreProfPos2NS(const ProfPos &PPA, const ProfPos &PPB);
SCORE ScoreProfPos2SP(const ProfPos &PPA, const ProfPos &PPB);
SCORE ScoreProfPos2SPN(const ProfPos &PPA, const ProfPos &PPB);
void AnchoredProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut);
void SetProfileProfileAlphabet(MSA &msa1, MSA &msa2);
} // namespace muscle
#endif // FastProf_h
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