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#ifndef FastProf2_h
#define FastProf2_h
#include "msa.h"
#include "pwpath.h"
#include <math.h> // for log function
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;
};
const unsigned RESIDUE_GROUP_MULTIPLE = (unsigned) ~0;
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);
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 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);
void SetScoreMatrix();
extern bool IsHydrophobic(const FCOUNT fcCounts[]);
void Hydro(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);
#endif // FastProf_h
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