nwdasmall.cpp

unix,linux下编译。用于蛋白质

#include "muscle.h"
#include <math.h>
#include "pwpath.h"
#include "profile.h"
#include <stdio.h>

#if	DOUBLE_AFFINE

// NW double affine small memory, term gaps fully penalized
// (so up to caller to adjust in profile if desired).

#define	TRACE	0

#define MIN(x, y)	((x) < (y) ? (x) : (y))

#if	TRACE
extern bool g_bKeepSimpleDP;
extern SCORE *g_DPM;
extern SCORE *g_DPD;
extern SCORE *g_DPE;
extern SCORE *g_DPI;
extern SCORE *g_DPJ;
extern char *g_TBM;
extern char *g_TBD;
extern char *g_TBE;
extern char *g_TBI;
extern char *g_TBJ;
#endif

#if	TRACE
#define ALLOC_TRACE()								\
	const SCORE UNINIT = MINUS_INFINITY;			\
	const size_t LM = uPrefixCountA*uPrefixCountB;	\
													\
	SCORE *DPM_ = new SCORE[LM];					\
	SCORE *DPD_ = new SCORE[LM];					\
	SCORE *DPE_ = new SCORE[LM];					\
	SCORE *DPI_ = new SCORE[LM];					\
	SCORE *DPJ_ = new SCORE[LM];					\
													\
	char *TBM_ = new char[LM];						\
	char *TBD_ = new char[LM];						\
	char *TBE_ = new char[LM];						\
	char *TBI_ = new char[LM];						\
	char *TBJ_ = new char[LM];						\
													\
	memset(TBM_, '?', LM);							\
	memset(TBD_, '?', LM);							\
	memset(TBE_, '?', LM);							\
	memset(TBI_, '?', LM);							\
	memset(TBJ_, '?', LM);							\
													\
	for (unsigned i = 0; i <= uLengthA; ++i)		\
		for (unsigned j = 0; j <= uLengthB; ++j)	\
			{										\
			DPM(i, j) = UNINIT;						\
			DPD(i, j) = UNINIT;						\
			DPE(i, j) = UNINIT;						\
			DPI(i, j) = UNINIT;						\
			DPJ(i, j) = UNINIT;						\
			}
#else
#define ALLOC_TRACE()
#endif

#if	TRACE
#define SetDPM(i, j, x)		DPM(i, j) = x
#define SetDPD(i, j, x)		DPD(i, j) = x
#define SetDPE(i, j, x)		DPE(i, j) = x
#define SetDPI(i, j, x)		DPI(i, j) = x
#define SetDPJ(i, j, x)		DPJ(i, j) = x
#define SetTBM(i, j, x)		TBM(i, j) = x
#define SetTBD(i, j, x)		TBD(i, j) = x
#define SetTBE(i, j, x)		TBE(i, j) = x
#define SetTBI(i, j, x)		TBI(i, j) = x
#define SetTBJ(i, j, x)		TBJ(i, j) = x
#else
#define SetDPM(i, j, x)		/* empty  */
#define SetDPD(i, j, x)		/* empty  */
#define SetDPE(i, j, x)		/* empty  */
#define SetDPI(i, j, x)		/* empty  */
#define SetDPJ(i, j, x)		/* empty  */
#define SetTBM(i, j, x)		/* empty  */
#define SetTBD(i, j, x)		/* empty  */
#define SetTBE(i, j, x)		/* empty  */
#define SetTBI(i, j, x)		/* empty  */
#define SetTBJ(i, j, x)		/* empty  */
#endif

#define RECURSE_D(i, j)				\
	{								\
	SCORE DD = DRow[j] + e;			\
	SCORE MD = MPrev[j] + PA[i-1].m_scoreGapOpen;\
	if (DD > MD)					\
		{							\
		DRow[j] = DD;				\
		SetTBD(i, j, 'D');			\
		}							\
	else							\
		{							\
		DRow[j] = MD;				\
		SetBitTBD(TB, i, j, 'M');	\
		SetTBD(i, j, 'M');			\
		}							\
	SetDPD(i, j, DRow[j]);			\
	}

#define RECURSE_E(i, j)				\
	{								\
	SCORE EE = ERow[j] + e2;		\
	SCORE ME = MPrev[j] + PA[i-1].m_scoreGapOpen2;\
	if (EE > ME)					\
		{							\
		ERow[j] = EE;				\
		SetTBE(i, j, 'E');			\
		}							\
	else							\
		{							\
		ERow[j] = ME;				\
		SetBitTBE(TB, i, j, 'M');	\
		SetTBE(i, j, 'M');			\
		}							\
	SetDPE(i, j, ERow[j]);			\
	}

#define RECURSE_D_ATerm(j)	RECURSE_D(uLengthA, j)
#define RECURSE_E_ATerm(j)	RECURSE_E(uLengthA, j)

#define RECURSE_D_BTerm(j)	RECURSE_D(i, uLengthB)
#define RECURSE_E_BTerm(j)	RECURSE_E(i, uLengthB)

#define RECURSE_I(i, j)				\
	{								\
	Iij += e;						\
	SCORE MI = MCurr[j-1] + PB[j-1].m_scoreGapOpen;\
	if (MI >= Iij)					\
		{							\
		Iij = MI;					\
		SetBitTBI(TB, i, j, 'M');	\
		SetTBI(i, j, 'M');			\
		}							\
	else							\
		SetTBI(i, j, 'I');			\
	SetDPI(i, j, Iij);				\
	}

#define RECURSE_J(i, j)				\
	{								\
	Jij += e2;						\
	SCORE MJ = MCurr[j-1] + PB[j-1].m_scoreGapOpen2;\
	if (MJ >= Jij)					\
		{							\
		Jij = MJ;					\
		SetBitTBJ(TB, i, j, 'M');	\
		SetTBJ(i, j, 'M');			\
		}							\
	else							\
		SetTBJ(i, j, 'I');			\
	SetDPJ(i, j, Jij);				\
	}

#define RECURSE_I_ATerm(j)	RECURSE_I(uLengthA, j)
#define RECURSE_J_ATerm(j)	RECURSE_J(uLengthA, j)

#define RECURSE_I_BTerm(j)	RECURSE_I(i, uLengthB)
#define RECURSE_J_BTerm(j)	RECURSE_J(i, uLengthB)

#define RECURSE_M(i, j)									\
	{													\
	SCORE Best = MCurr[j];  /*  MM  */					\
	SetTBM(i+1, j+1, 'M');								\
	SetBitTBM(TB, i+1, j+1, 'M');						\
														\
	SCORE DM = DRow[j] + PA[i-1].m_scoreGapClose;		\
	if (DM > Best)										\
		{												\
		Best = DM;										\
		SetTBM(i+1, j+1, 'D');							\
		SetBitTBM(TB, i+1, j+1, 'D');					\
		}												\
														\
	SCORE EM = ERow[j] + PA[i-1].m_scoreGapClose2;		\
	if (EM > Best)										\
		{												\
		Best = EM;										\
		SetTBM(i+1, j+1, 'E');							\
		SetBitTBM(TB, i+1, j+1, 'E');					\
		}												\
														\
	SCORE IM = Iij + PB[j-1].m_scoreGapClose;			\
	if (IM > Best)										\
		{												\
		Best = IM;										\
		SetTBM(i+1, j+1, 'I');							\
		SetBitTBM(TB, i+1, j+1, 'I');					\
		}												\
														\
	SCORE JM = Jij + PB[j-1].m_scoreGapClose2;			\
	if (JM > Best)										\
		{												\
		Best = JM;										\
		SetTBM(i+1, j+1, 'J');							\
		SetBitTBM(TB, i+1, j+1, 'J');					\
		}												\
	MNext[j+1] += Best;									\
	SetDPM(i+1, j+1, MNext[j+1]);						\
	}

#if	TRACE
static bool LocalEq(BASETYPE b1, BASETYPE b2)
	{
	if (b1 < -100000 && b2 < -100000)
		return true;
	double diff = fabs(b1 - b2);
	if (diff < 0.0001)
		return true;
	double sum = fabs(b1) + fabs(b2);
	return diff/sum < 0.005;
	}

static char Get_M_Char(char Bits)
	{
	switch (Bits & BIT_xM)
		{
	case BIT_MM:
		return 'M';
	case BIT_DM:
		return 'D';
	case BIT_EM:
		return 'E';
	case BIT_IM:
		return 'I';
	case BIT_JM:
		return 'J';
		}
	Quit("Huh?");
	return '?';
	}

static char Get_D_Char(char Bits)
	{
	return (Bits & BIT_xD) ? 'M' : 'D';
	}

static char Get_E_Char(char Bits)
	{
	return (Bits & BIT_xE) ? 'M' : 'E';
	}

static char Get_I_Char(char Bits)
	{
	return (Bits & BIT_xI) ? 'M' : 'I';
	}

static char Get_J_Char(char Bits)
	{
	return (Bits & BIT_xJ) ? 'M' : 'J';
	}

static bool DPEq(char c, SCORE *g_DP, SCORE *DPD_,
  unsigned uPrefixCountA, unsigned uPrefixCountB)
	{
	if (0 == g_DP)
		{
		Log("***DPDIFF*** DP%c=NULL\n", c);
		return true;
		}

	SCORE *DPM_ = g_DP;
	for (unsigned i = 0; i < uPrefixCountA; ++i)
		for (unsigned j = 0; j < uPrefixCountB; ++j)
			if (!LocalEq(DPM(i, j), DPD(i, j)))
				{
				Log("***DPDIFF*** DP%c(%d, %d) Simple = %.2g, Small = %.2g\n",
				  c, i, j, DPM(i, j), DPD(i, j));
				return false;
				}
	return true;
	}

static bool CompareTB(char **TB, char *TBM_, char *TBD_, char *TBE_, char *TBI_, char *TBJ_,
  unsigned uPrefixCountA, unsigned uPrefixCountB)
	{
	if (!g_bKeepSimpleDP)
		return true;
	SCORE *DPM_ = g_DPM;
	bool Eq = true;
	for (unsigned i = 0; i < uPrefixCountA; ++i)
		for (unsigned j = 0; j < uPrefixCountB; ++j)
			{
			char c1 = TBM(i, j);
			char c2 = Get_M_Char(TB[i][j]);
			if (c1 != '?' && c1 != c2 && DPM(i, j) > -100000)
				{
				Log("TBM(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
				Eq = false;
				goto D;
				}
			}

D:
	SCORE *DPD_ = g_DPD;
	for (unsigned i = 0; i < uPrefixCountA; ++i)
		for (unsigned j = 0; j < uPrefixCountB; ++j)
			{
			char c1 = TBD(i, j);
			char c2 = Get_D_Char(TB[i][j]);
			if (c1 != '?' && c1 != c2 && DPD(i, j) > -100000)
				{
				Log("TBD(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
				Eq = false;
				goto E;
				}
			}
E:
	SCORE *DPE_ = g_DPE;
	if (0 == TBE_)
		goto I;
	for (unsigned i = 0; i < uPrefixCountA; ++i)
		for (unsigned j = 0; j < uPrefixCountB; ++j)
			{
			char c1 = TBE(i, j);
			char c2 = Get_E_Char(TB[i][j]);
			if (c1 != '?' && c1 != c2 && DPE(i, j) > -100000)
				{
				Log("TBE(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
				Eq = false;
				goto I;
				}
			}
I:
	SCORE *DPI_ = g_DPI;
	for (unsigned i = 0; i < uPrefixCountA; ++i)
		for (unsigned j = 0; j < uPrefixCountB; ++j)
			{
			char c1 = TBI(i, j);
			char c2 = Get_I_Char(TB[i][j]);
			if (c1 != '?' && c1 != c2 && DPI(i, j) > -100000)
				{
				Log("TBI(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
				Eq = false;
				goto J;
				}
			}
J:
	SCORE *DPJ_ = g_DPJ;
	if (0 == DPJ_)
		goto Done;
	for (unsigned i = 0; i < uPrefixCountA; ++i)
		for (unsigned j = 0; j < uPrefixCountB; ++j)
			{
			char c1 = TBJ(i, j);
			char c2 = Get_J_Char(TB[i][j]);
			if (c1 != '?' && c1 != c2 && DPJ(i, j) > -100000)
				{
				Log("TBJ(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
				Eq = false;
				goto Done;
				}
			}
Done:
	if (Eq)
		Log("TB success\n");
	return Eq;
	}

static const char *LocalScoreToStr(SCORE s)
	{
	static char str[16];
	if (s < -100000)
		return "     *";
	sprintf(str, "%6.1f", s);
	return str;
	}

static void LogDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
  unsigned uPrefixCountA, unsigned uPrefixCountB)
	{
	Log("        ");
	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
		char c = ' ';
		if (uPrefixLengthB > 0)
			c = ConsensusChar(PB[uPrefixLengthB - 1]);
		Log(" %4u:%c", uPrefixLengthB, c);
		}
	Log("\n");
	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
		char c = ' ';
		if (uPrefixLengthA > 0)
			c = ConsensusChar(PA[uPrefixLengthA - 1]);
		Log("%4u:%c  ", uPrefixLengthA, c);
		for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
			Log(" %s", LocalScoreToStr(DPM(uPrefixLengthA, uPrefixLengthB)));
		Log("\n");
		}
	}

static void LogBitTB(char **TB, const ProfPos *PA, const ProfPos *PB,
  unsigned uPrefixCountA, unsigned uPrefixCountB)
	{
	Log("        ");
	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
		char c = ' ';
		if (uPrefixLengthB > 0)
			c = ConsensusChar(PB[uPrefixLengthB - 1]);
		Log(" %4u:%c", uPrefixLengthB, c);
		}
	Log("\n");
	Log("Bit TBM:\n");
	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
		char c = ' ';
		if (uPrefixLengthA > 0)
			c = ConsensusChar(PA[uPrefixLengthA - 1]);
		Log("%4u:%c  ", uPrefixLengthA, c);
		for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
			{
			char c = Get_M_Char(TB[uPrefixLengthA][uPrefixLengthB]);
			Log(" %6c", c);
			}
		Log("\n");
		}

	Log("\n");
	Log("Bit TBD:\n");
	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
		char c = ' ';
		if (uPrefixLengthA > 0)
			c = ConsensusChar(PA[uPrefixLengthA - 1]);
		Log("%4u:%c  ", uPrefixLengthA, c);
		for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
			{
			char c = Get_D_Char(TB[uPrefixLengthA][uPrefixLengthB]);
			Log(" %6c", c);
			}
		Log("\n");
		}

	Log("\n");
	Log("Bit TBE:\n");
	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
		char c = ' ';
		if (uPrefixLengthA > 0)
			c = ConsensusChar(PA[uPrefixLengthA - 1]);
		Log("%4u:%c  ", uPrefixLengthA, c);
		for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
			{
			char c = Get_E_Char(TB[uPrefixLengthA][uPrefixLengthB]);
			Log(" %6c", c);
			}
		Log("\n");
		}

	Log("\n");
	Log("Bit TBI:\n");
	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
		char c = ' ';
		if (uPrefixLengthA > 0)
			c = ConsensusChar(PA[uPrefixLengthA - 1]);
		Log("%4u:%c  ", uPrefixLengthA, c);
		for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
			{
			char c = Get_I_Char(TB[uPrefixLengthA][uPrefixLengthB]);
			Log(" %6c", c);
			}
		Log("\n");
		}