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#ifndef dp_h
#define dp_h
#define SAVE_FAST 0
#include "myutils.h"
#include "mx.h"
#include "seqdb.h"
#include "diagbox.h"
#include "path.h"
#include "alnparams.h"
#include "alnheuristics.h"
#include "hspfinder.h"
typedef void (*OnPathFn)(const string &Path, bool Full);
enum XType
{
XType_Full=1,
XType_Fwd=2,
XType_Bwd=3,
};
// public
float ViterbiBrute(const byte *A, unsigned LA, const byte *B, unsigned LB,
unsigned DiagLo, unsigned DiagHi, const AlnParams &AP, PathData &PD);
float ViterbiSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, PathData &PD);
float ViterbiSimpleBand(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, unsigned DiagLo, unsigned DiagHi, PathData &PD);
float ViterbiFast(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, PathData &PD);
float ViterbiFastBand(const byte *A, unsigned LA, const byte *B, unsigned LB,
unsigned DiagLo, unsigned DiagHi, const AlnParams &AP, PathData &PD);
float ViterbiFastMainDiag(const byte *A, unsigned LA, const byte *B, unsigned LB,
unsigned BandRadius, const AlnParams &AP, PathData &PD);
float XDropFwdSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);
float XDropBwdSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);
float XDropFwdFast(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);
float XDropBwdFast(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);
void XDropAlign(const byte *A, unsigned LA, const byte *B, unsigned LB,
unsigned AncLoi, unsigned AncLoj, unsigned AncLen, const AlnParams &AP,
float XDrop, HSPData &HSP, PathData &PD);
float SWSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, unsigned &Loi, unsigned &Leni, unsigned &Lenj,
unsigned &Hij, PathData &PD);
float SWFast(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, unsigned &Loi, unsigned &Leni, unsigned &Lenj,
unsigned &Hij, PathData &PD);
void SWFast2(const SeqData &SA, const SeqData &SB, const AlnParams &AP,
HSPData &HSP, PathData &PD);
void SWSimple2(const SeqData &SA, const SeqData &SB, const AlnParams &AP,
HSPData &HSP, PathData &PD);
float SWUngapped(const byte *A, unsigned LA, const byte *B, unsigned LB,
const float * const *SubstMx, unsigned &LoA, unsigned &LoB, unsigned &Len);
void SWUngapped2(const SeqData &SA, const SeqData &SB, const AlnParams &AP,
HSPData &HSP);
float SWFastNTB(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP);
void GlobalAlignBand(const byte *A, unsigned LA, const byte *B, unsigned LB,
const AlnParams &AP, unsigned BandRadius, PathData &PD);
bool GlobalAlign(const SeqData &Query, const SeqData &Target, const AlnParams &AP,
const AlnHeuristics &AH, HSPFinder &HF, float MinFractId, float &HSPFractId,
PathData &PD);
bool GlobalAlign(const SeqData &Query, const SeqData &Target, string &Path);
void GetBruteMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);
void GetSimpleDPMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);
void GetSimpleBandMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);
void GetXDropFwdSimpleDPMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);
#if SAVE_FAST
void GetFastMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);
void GetFastBandMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);
#endif
// private
void TraceBackBit(unsigned LA, unsigned LB, char State, PathData &PD);
void TraceBackBitSW(unsigned LA, unsigned LB, unsigned Besti, unsigned Bestj,
unsigned &Leni, unsigned &Lenj, PathData &PD);
void EnumPaths(unsigned L1, unsigned L2, bool SubPaths, OnPathFn OnPath);
void AllocBit(unsigned LA, unsigned LB);
const byte TRACEBITS_DM = 0x01;
const byte TRACEBITS_IM = 0x02;
const byte TRACEBITS_MD = 0x04;
const byte TRACEBITS_MI = 0x08;
const byte TRACEBITS_SM = 0x10;
const byte TRACEBITS_UNINIT = ~0x1f;
extern Mx<byte> g_Mx_TBBit;
extern float *g_DPRow1;
extern float *g_DPRow2;
extern byte **g_TBBit;
static inline void Max_xM(float &Score, float MM, float DM, float IM, byte &State)
{
Score = MM;
State = 'M';
if (DM > Score)
{
Score = DM;
State = 'D';
}
if (IM > Score)
{
Score = IM;
State = 'I';
}
}
static inline void Max_xD(float &Score, float MD, float DD, byte &State)
{
if (MD >= DD)
{
Score = MD;
State = 'M';
}
else
{
Score = DD;
State = 'D';
}
}
static inline void Max_xI(float &Score, float MI, float II, byte &State)
{
if (MI >= II)
{
Score = MI;
State = 'M';
}
else
{
Score = II;
State = 'I';
}
}
#endif // dp_h
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