示例#1
0
SCORE TraceBack(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, const SCORE *DPM_, const SCORE *DPD_, const SCORE *DPI_,
  PWPath &Path)
	{
#if	TRACE
	Log("\n");
	Log("TraceBack LengthA=%u LengthB=%u\n", uLengthA, uLengthB);
#endif
	assert(uLengthB > 0 && uLengthA > 0);

	const unsigned uPrefixCountA = uLengthA + 1;
	const unsigned uPrefixCountB = uLengthB + 1;

	Path.Clear();

	unsigned uPrefixLengthA = uLengthA;
	unsigned uPrefixLengthB = uLengthB;

	const SCORE scoreM = DPM(uPrefixLengthA, uPrefixLengthB);
	SCORE scoreD = DPD(uPrefixLengthA, uPrefixLengthB);
	SCORE scoreI = DPI(uPrefixLengthA, uPrefixLengthB);

	const ProfPos &LastPPA = PA[uLengthA - 1];
	const ProfPos &LastPPB = PB[uLengthB - 1];

	scoreD += LastPPA.m_scoreGapClose;
	scoreI += LastPPB.m_scoreGapClose;

	char cEdgeType = cInsane;
	SCORE scoreMax;
	if (scoreM >= scoreD && scoreM >= scoreI)
		{
		scoreMax = scoreM;
		cEdgeType = 'M';
		}
	else if (scoreD >= scoreM && scoreD >= scoreI)
		{
		scoreMax = scoreD;
		cEdgeType = 'D';
		}
	else
		{
		assert(scoreI >= scoreM && scoreI >= scoreD);
		scoreMax = scoreI;
		cEdgeType = 'I';
		}

	for (;;)
		{
		if ('S' == cEdgeType)
			break;

		PWEdge Edge;
		Edge.cType = cEdgeType;
		Edge.uPrefixLengthA = uPrefixLengthA;
		Edge.uPrefixLengthB = uPrefixLengthB;
		Path.PrependEdge(Edge);

		char cPrevEdgeType;
		unsigned uPrevPrefixLengthA = uPrefixLengthA;
		unsigned uPrevPrefixLengthB = uPrefixLengthB;

		switch (cEdgeType)
			{
		case 'M':
			{
			assert(uPrefixLengthA > 0);
			assert(uPrefixLengthB > 0);
			const ProfPos &PPA = PA[uPrefixLengthA - 1];
			const ProfPos &PPB = PB[uPrefixLengthB - 1];

			const SCORE Score = DPM(uPrefixLengthA, uPrefixLengthB);
			const SCORE scoreMatch = ScoreProfPos2(PPA, PPB);

			SCORE scoreSM;
			if (1 == uPrefixLengthA && 1 == uPrefixLengthB)
				scoreSM = scoreMatch;
			else
				scoreSM = MINUS_INFINITY;

			SCORE scoreMM = MINUS_INFINITY;
			SCORE scoreDM = MINUS_INFINITY;
			SCORE scoreIM = MINUS_INFINITY;
			if (uPrefixLengthA > 1 && uPrefixLengthB > 1)
				scoreMM = DPM(uPrefixLengthA-1, uPrefixLengthB-1) + scoreMatch;
			if (uPrefixLengthA > 1)
				{
				SCORE scoreTransDM = PA[uPrefixLengthA-2].m_scoreGapClose;
				scoreDM = DPD(uPrefixLengthA-1, uPrefixLengthB-1) + scoreTransDM + scoreMatch;
				}
			if (uPrefixLengthB > 1)
				{
				SCORE scoreTransIM = PB[uPrefixLengthB-2].m_scoreGapClose;
				scoreIM = DPI(uPrefixLengthA-1, uPrefixLengthB-1) + scoreTransIM + scoreMatch;
				}

			if (EQ(scoreMM, Score))
				cPrevEdgeType = 'M';
			else if (EQ(scoreDM, Score))
				cPrevEdgeType = 'D';
			else if (EQ(scoreIM, Score))
				cPrevEdgeType = 'I';
			else if (EQ(scoreSM, Score))
				cPrevEdgeType = 'S';
			else
				Quit("TraceBack: failed to match M score=%g M=%g D=%g I=%g S=%g",
				  Score, scoreMM, scoreDM, scoreIM, scoreSM);

			--uPrevPrefixLengthA;
			--uPrevPrefixLengthB;
			break;
			}

		case 'D':
			{
			assert(uPrefixLengthA > 0);
			const SCORE Score = DPD(uPrefixLengthA, uPrefixLengthB);

			SCORE scoreMD = MINUS_INFINITY;
			SCORE scoreDD = MINUS_INFINITY;
			SCORE scoreSD = MINUS_INFINITY;
			if (uPrefixLengthB == 0)
				{
				if (uPrefixLengthA == 1)
					scoreSD = PA[0].m_scoreGapOpen;
				else
					scoreSD = DPD(uPrefixLengthA - 1, 0);
				}
			if (uPrefixLengthA > 1)
				{
				const ProfPos &PPA = PA[uPrefixLengthA - 1];
				SCORE scoreTransMD = PPA.m_scoreGapOpen;
				scoreMD = DPM(uPrefixLengthA-1, uPrefixLengthB) + scoreTransMD;
				scoreDD = DPD(uPrefixLengthA-1, uPrefixLengthB);
				}

			if (EQ(Score, scoreMD))
				cPrevEdgeType = 'M';
			else if (EQ(Score, scoreDD))
				cPrevEdgeType = 'D';
			else if (EQ(Score, scoreSD))
				cPrevEdgeType = 'S';
			else
				Quit("TraceBack: failed to match D");

			--uPrevPrefixLengthA;
			break;
			}

		case 'I':
			{
			assert(uPrefixLengthB > 0);
			const SCORE Score = DPI(uPrefixLengthA, uPrefixLengthB);

			SCORE scoreMI = MINUS_INFINITY;
			SCORE scoreII = MINUS_INFINITY;
			SCORE scoreSI = MINUS_INFINITY;
			if (uPrefixLengthA == 0)
				{
				if (uPrefixLengthB == 1)
					scoreSI = PB[0].m_scoreGapOpen;
				else
					scoreSI = DPI(0, uPrefixLengthB - 1);
				}
			if (uPrefixLengthB > 1)
				{
				const ProfPos &PPB = PB[uPrefixLengthB - 1];
				SCORE scoreTransMI = PPB.m_scoreGapOpen;
				scoreMI = DPM(uPrefixLengthA, uPrefixLengthB-1) + scoreTransMI;
				scoreII = DPI(uPrefixLengthA, uPrefixLengthB-1);
				}

			if (EQ(Score, scoreMI))
				cPrevEdgeType = 'M';
			else if (EQ(Score, scoreII))
				cPrevEdgeType = 'I';
			else if (EQ(Score, scoreSI))
				cPrevEdgeType = 'S';
			else
				Quit("TraceBack: failed to match I");

			--uPrevPrefixLengthB;
			break;
			}

		default:
			assert(false);
			}
#if	TRACE
		Log("Edge %c%c%u.%u", cPrevEdgeType, cEdgeType, uPrefixLengthA, uPrefixLengthB);
		Log("\n");
#endif
		cEdgeType = cPrevEdgeType;
		uPrefixLengthA = uPrevPrefixLengthA;
		uPrefixLengthB = uPrevPrefixLengthB;
		}

	return scoreMax;
	}
示例#2
0
SCORE ObjScoreDP_Profs(const ProfPos *PA, const ProfPos *PB, unsigned uColCount,
  SCORE MatchScore[])
	{
//#if	TRACE
//	Log("Profile 1:\n");
//	ListProfile(PA, uColCount, &msa1);
//
//	Log("Profile 2:\n");
//	ListProfile(PB, uColCount, &msa2);
//#endif

	SCORE scoreTotal = 0;

	for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
		{
		const ProfPos &PPA = PA[uColIndex];
		const ProfPos &PPB = PB[uColIndex];

		SCORE scoreGap = 0;
		SCORE scoreMatch = 0;
	// If gapped column...
		if (PPA.m_bAllGaps && PPB.m_bAllGaps)
			scoreGap = 0;
		else if (PPA.m_bAllGaps)
			{
			if (uColCount - 1 == uColIndex || !PA[uColIndex+1].m_bAllGaps)
				scoreGap = PPB.m_scoreGapClose;
			if (0 == uColIndex || !PA[uColIndex-1].m_bAllGaps)
				scoreGap += PPB.m_scoreGapOpen;
			//if (0 == scoreGap)
			//	scoreGap = PPB.m_scoreGapExtend;
			}
		else if (PPB.m_bAllGaps)
			{
			if (uColCount - 1 == uColIndex || !PB[uColIndex+1].m_bAllGaps)
				scoreGap = PPA.m_scoreGapClose;
			if (0 == uColIndex || !PB[uColIndex-1].m_bAllGaps)
				scoreGap += PPA.m_scoreGapOpen;
			//if (0 == scoreGap)
			//	scoreGap = PPA.m_scoreGapExtend;
			}
		else
			scoreMatch = ScoreProfPos2(PPA, PPB);

		if (0 != MatchScore)
			MatchScore[uColIndex] = scoreMatch;

		scoreTotal += scoreMatch + scoreGap;

		extern bool g_bTracePPScore;
		extern MSA *g_ptrPPScoreMSA1;
		extern MSA *g_ptrPPScoreMSA2;
		if (g_bTracePPScore)
			{
			const MSA &msa1 = *g_ptrPPScoreMSA1;
			const MSA &msa2 = *g_ptrPPScoreMSA2;
			const unsigned uSeqCount1 = msa1.GetSeqCount();
			const unsigned uSeqCount2 = msa2.GetSeqCount();

			for (unsigned n = 0; n < uSeqCount1; ++n)
				Log("%c", msa1.GetChar(n, uColIndex));
			Log("  ");
			for (unsigned n = 0; n < uSeqCount2; ++n)
				Log("%c", msa2.GetChar(n, uColIndex));
			Log("  %10.3f", scoreMatch);
			if (scoreGap != 0)
				Log("  %10.3f", scoreGap);
			Log("\n");
			}
		}

	delete[] PA;
	delete[] PB;

	return scoreTotal;
	}
示例#3
0
SCORE NWDASimple(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
	assert(uLengthB > 0 && uLengthA > 0);

	const unsigned uPrefixCountA = uLengthA + 1;
	const unsigned uPrefixCountB = uLengthB + 1;

// Allocate DP matrices
	const size_t LM = uPrefixCountA*uPrefixCountB;
	SCORE *DPL_ = new SCORE[LM];
	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);

	DPM(0, 0) = 0;
	DPD(0, 0) = MINUS_INFINITY;
	DPE(0, 0) = MINUS_INFINITY;
	DPI(0, 0) = MINUS_INFINITY;
	DPJ(0, 0) = MINUS_INFINITY;

	DPM(1, 0) = MINUS_INFINITY;
	DPD(1, 0) = PA[0].m_scoreGapOpen;
	DPE(1, 0) = PA[0].m_scoreGapOpen2;
	TBD(1, 0) = 'D';
	TBE(1, 0) = 'E';
	DPI(1, 0) = MINUS_INFINITY;
	DPJ(1, 0) = MINUS_INFINITY;

	DPM(0, 1) = MINUS_INFINITY;
	DPD(0, 1) = MINUS_INFINITY;
	DPE(0, 1) = MINUS_INFINITY;
	DPI(0, 1) = PB[0].m_scoreGapOpen;
	DPJ(0, 1) = PB[0].m_scoreGapOpen2;
	TBI(0, 1) = 'I';
	TBJ(0, 1) = 'J';

// Empty prefix of B is special case
	for (unsigned uPrefixLengthA = 2; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
		DPM(uPrefixLengthA, 0) = MINUS_INFINITY;

		DPD(uPrefixLengthA, 0) = DPD(uPrefixLengthA - 1, 0) + g_scoreGapExtend.get();
		DPE(uPrefixLengthA, 0) = DPE(uPrefixLengthA - 1, 0) + g_scoreGapExtend2.get();

		TBD(uPrefixLengthA, 0) = 'D';
		TBE(uPrefixLengthA, 0) = 'E';

		DPI(uPrefixLengthA, 0) = MINUS_INFINITY;
		DPJ(uPrefixLengthA, 0) = MINUS_INFINITY;
		}

// Empty prefix of A is special case
	for (unsigned uPrefixLengthB = 2; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
		DPM(0, uPrefixLengthB) = MINUS_INFINITY;

		DPD(0, uPrefixLengthB) = MINUS_INFINITY;
		DPE(0, uPrefixLengthB) = MINUS_INFINITY;

		DPI(0, uPrefixLengthB) = DPI(0, uPrefixLengthB - 1) + g_scoreGapExtend.get();
		DPJ(0, uPrefixLengthB) = DPJ(0, uPrefixLengthB - 1) + g_scoreGapExtend2.get();

		TBI(0, uPrefixLengthB) = 'I';
		TBJ(0, uPrefixLengthB) = 'J';
		}

// Special case to agree with NWFast, no D-I transitions so...
	DPD(uLengthA, 0) = MINUS_INFINITY;
	DPE(uLengthA, 0) = MINUS_INFINITY;
//	DPI(0, uLengthB) = MINUS_INFINITY;
//	DPJ(0, uLengthB) = MINUS_INFINITY;

// ============
// Main DP loop
// ============
	SCORE scoreGapCloseB = MINUS_INFINITY;
	SCORE scoreGapClose2B = MINUS_INFINITY;
	for (unsigned uPrefixLengthB = 1; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
		const ProfPos &PPB = PB[uPrefixLengthB - 1];

		SCORE scoreGapCloseA = MINUS_INFINITY;
		SCORE scoreGapClose2A = MINUS_INFINITY;
		for (unsigned uPrefixLengthA = 1; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
			{
			const ProfPos &PPA = PA[uPrefixLengthA - 1];

			{
		// Match M=LetterA+LetterB
			SCORE scoreLL = ScoreProfPos2(PPA, PPB);
			DPL(uPrefixLengthA, uPrefixLengthB) = scoreLL;

			SCORE scoreMM = DPM(uPrefixLengthA-1, uPrefixLengthB-1);
			SCORE scoreDM = DPD(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseA;
			SCORE scoreEM = DPE(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapClose2A;
			SCORE scoreIM = DPI(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseB;
			SCORE scoreJM = DPJ(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapClose2B;

			SCORE scoreBest;
			if (scoreMM >= scoreDM && scoreMM >= scoreEM && scoreMM >= scoreIM && scoreMM >= scoreJM)
				{
				scoreBest = scoreMM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else if (scoreDM >= scoreMM && scoreDM >= scoreEM && scoreDM >= scoreIM && scoreDM >= scoreJM)
				{
				scoreBest = scoreDM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'D';
				}
			else if (scoreEM >= scoreMM && scoreEM >= scoreDM && scoreEM >= scoreIM && scoreEM >= scoreJM)
				{
				scoreBest = scoreEM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'E';
				}
			else if (scoreIM >= scoreMM && scoreIM >= scoreDM && scoreIM >= scoreEM && scoreIM >= scoreJM)
				{
				scoreBest = scoreIM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'I';
				}
			else
				{
				assert(scoreJM >= scoreMM && scoreJM >= scoreDM && scoreJM >= scoreEM && scoreJM >= scoreIM);
				scoreBest = scoreJM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'J';
				}
			DPM(uPrefixLengthA, uPrefixLengthB) = scoreBest + scoreLL;
			}

			{
		// Delete D=LetterA+GapB
			SCORE scoreMD = DPM(uPrefixLengthA-1, uPrefixLengthB) +
			  PA[uPrefixLengthA-1].m_scoreGapOpen;
			SCORE scoreDD = DPD(uPrefixLengthA-1, uPrefixLengthB) + g_scoreGapExtend.get();

			SCORE scoreBest;
			if (scoreMD >= scoreDD)
				{
				scoreBest = scoreMD;
				TBD(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else
				{
				assert(scoreDD >= scoreMD);
				scoreBest = scoreDD;
				TBD(uPrefixLengthA, uPrefixLengthB) = 'D';
				}
			DPD(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

			{
		// Delete E=LetterA+GapB
			SCORE scoreME = DPM(uPrefixLengthA-1, uPrefixLengthB) +
			  PA[uPrefixLengthA-1].m_scoreGapOpen2;
			SCORE scoreEE = DPE(uPrefixLengthA-1, uPrefixLengthB) + g_scoreGapExtend2.get();

			SCORE scoreBest;
			if (scoreME >= scoreEE)
				{
				scoreBest = scoreME;
				TBE(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else
				{
				assert(scoreEE >= scoreME);
				scoreBest = scoreEE;
				TBE(uPrefixLengthA, uPrefixLengthB) = 'E';
				}
			DPE(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

		// Insert I=GapA+LetterB
			{
			SCORE scoreMI = DPM(uPrefixLengthA, uPrefixLengthB-1) +
			  PB[uPrefixLengthB - 1].m_scoreGapOpen;
			SCORE scoreII = DPI(uPrefixLengthA, uPrefixLengthB-1) + g_scoreGapExtend.get();

			SCORE scoreBest;
			if (scoreMI >= scoreII)
				{
				scoreBest = scoreMI;
				TBI(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else 
				{
				assert(scoreII > scoreMI);
				scoreBest = scoreII;
				TBI(uPrefixLengthA, uPrefixLengthB) = 'I';
				}
			DPI(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

		// Insert J=GapA+LetterB
			{
			SCORE scoreMJ = DPM(uPrefixLengthA, uPrefixLengthB-1) +
			  PB[uPrefixLengthB - 1].m_scoreGapOpen2;
			SCORE scoreJJ = DPJ(uPrefixLengthA, uPrefixLengthB-1) + g_scoreGapExtend2.get();

			SCORE scoreBest;
			if (scoreMJ >= scoreJJ)
				{
				scoreBest = scoreMJ;
				TBJ(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else 
				{
				assert(scoreJJ > scoreMJ);
				scoreBest = scoreJJ;
				TBJ(uPrefixLengthA, uPrefixLengthB) = 'J';
				}
			DPJ(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

			scoreGapCloseA = PPA.m_scoreGapClose;
			scoreGapClose2A = PPA.m_scoreGapClose2;
			}
		scoreGapCloseB = PPB.m_scoreGapClose;
		scoreGapClose2B = PPB.m_scoreGapClose2;
		}

#if TRACE
	Log("\n");
	Log("DA Simple DPL:\n");
	ListDP(DPL_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPM:\n");
	ListDP(DPM_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPD:\n");
	ListDP(DPD_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPE:\n");
	ListDP(DPE_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPI:\n");
	ListDP(DPI_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPJ:\n");
	ListDP(DPJ_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBM:\n");
	ListTB(TBM_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBD:\n");
	ListTB(TBD_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBE:\n");
	ListTB(TBE_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBI:\n");
	ListTB(TBI_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBJ:\n");
	ListTB(TBJ_, PA, PB, uPrefixCountA, uPrefixCountB);
#endif

// Trace-back
// ==========
	Path.Clear();

// Find last edge
	SCORE M = DPM(uLengthA, uLengthB);
	SCORE D = DPD(uLengthA, uLengthB) + PA[uLengthA-1].m_scoreGapClose;
	SCORE E = DPE(uLengthA, uLengthB) + PA[uLengthA-1].m_scoreGapClose2;
	SCORE I = DPI(uLengthA, uLengthB) + PB[uLengthB-1].m_scoreGapClose;
	SCORE J = DPJ(uLengthA, uLengthB) + PB[uLengthB-1].m_scoreGapClose2;
	char cEdgeType = '?';

	SCORE BestScore = M;
	cEdgeType = 'M';
	if (D > BestScore)
		{
		cEdgeType = 'D';
		BestScore = D;
		}
	if (E > BestScore)
		{
		cEdgeType = 'E';
		BestScore = E;
		}
	if (I > BestScore)
		{
		cEdgeType = 'I';
		BestScore = I;
		}
	if (J > BestScore)
		{
		cEdgeType = 'J';
		BestScore = J;
		}

#if	TRACE
	Log("DA Simple: MAB=%.4g DAB=%.4g EAB=%.4g IAB=%.4g JAB=%.4g best=%c\n",
	  M, D, E, I, J, cEdgeType);
#endif

	unsigned PLA = uLengthA;
	unsigned PLB = uLengthB;
	for (;;)
		{
		PWEdge Edge;
		Edge.cType = XlatEdgeType(cEdgeType);
		Edge.uPrefixLengthA = PLA;
		Edge.uPrefixLengthB = PLB;
#if	TRACE
		Log("Prepend %c%d.%d\n", Edge.cType, PLA, PLB);
#endif
		Path.PrependEdge(Edge);

		switch (cEdgeType)
			{
		case 'M':
			assert(PLA > 0);
			assert(PLB > 0);
			cEdgeType = TBM(PLA, PLB);
			--PLA;
			--PLB;
			break;

		case 'D':
			assert(PLA > 0);
			cEdgeType = TBD(PLA, PLB);
			--PLA;
			break;

		case 'E':
			assert(PLA > 0);
			cEdgeType = TBE(PLA, PLB);
			--PLA;
			break;

		case 'I':
			assert(PLB > 0);
			cEdgeType = TBI(PLA, PLB);
			--PLB;
			break;
		
		case 'J':
			assert(PLB > 0);
			cEdgeType = TBJ(PLA, PLB);
			--PLB;
			break;

		default:
			Quit("Invalid edge %c", cEdgeType);
			}
		if (0 == PLA && 0 == PLB)
			break;
		}
	Path.Validate();

//	SCORE Score = TraceBack(PA, uLengthA, PB, uLengthB, DPM_, DPD_, DPI_, Path);

#if	TRACE
	SCORE scorePath = FastScorePath2(PA, uLengthA, PB, uLengthB, Path);
	Path.LogMe();
	Log("Score = %s Path = %s\n", LocalScoreToStr(BestScore), LocalScoreToStr(scorePath));
#endif

	if (g_bKeepSimpleDP.get())
		{
		g_DPM.get() = DPM_;
		g_DPD.get() = DPD_;
		g_DPE.get() = DPE_;
		g_DPI.get() = DPI_;
		g_DPJ.get() = DPJ_;

		g_TBM.get() = TBM_;
		g_TBD.get() = TBD_;
		g_TBE.get() = TBE_;
		g_TBI.get() = TBI_;
		g_TBJ.get() = TBJ_;
		}
	else
		{
		delete[] DPM_;
		delete[] DPD_;
		delete[] DPE_;
		delete[] DPI_;
		delete[] DPJ_;

		delete[] TBM_;
		delete[] TBD_;
		delete[] TBE_;
		delete[] TBI_;
		delete[] TBJ_;
		}

	return BestScore;
	}
示例#4
0
文件: sw.cpp 项目: Unode/ext_apps
SCORE SW(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
	assert(uLengthB > 0 && uLengthA > 0);

	const unsigned uPrefixCountA = uLengthA + 1;
	const unsigned uPrefixCountB = uLengthB + 1;

// Allocate DP matrices
	const size_t LM = uPrefixCountA*uPrefixCountB;
	SCORE *DPM_ = new SCORE[LM];
	SCORE *DPD_ = new SCORE[LM];
	SCORE *DPI_ = new SCORE[LM];

	DPM(0, 0) = 0;
	DPD(0, 0) = MINUS_INFINITY;
	DPI(0, 0) = MINUS_INFINITY;

	DPM(1, 0) = MINUS_INFINITY;
	DPD(1, 0) = MINUS_INFINITY;
	DPI(1, 0) = MINUS_INFINITY;

	DPM(0, 1) = MINUS_INFINITY;
	DPD(0, 1) = MINUS_INFINITY;
	DPI(0, 1) = MINUS_INFINITY;

// Empty prefix of B is special case
	for (unsigned uPrefixLengthA = 2; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
	// M=LetterA+LetterB, impossible with empty prefix
		DPM(uPrefixLengthA, 0) = MINUS_INFINITY;

	// D=LetterA+GapB, never optimal in local alignment with gap penalties
		DPD(uPrefixLengthA, 0) = MINUS_INFINITY;

	// I=GapA+LetterB, impossible with empty prefix
		DPI(uPrefixLengthA, 0) = MINUS_INFINITY;
		}

// Empty prefix of A is special case
	for (unsigned uPrefixLengthB = 2; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
	// M=LetterA+LetterB, impossible with empty prefix
		DPM(0, uPrefixLengthB) = MINUS_INFINITY;

	// D=LetterA+GapB, impossible with empty prefix
		DPD(0, uPrefixLengthB) = MINUS_INFINITY;

	// I=GapA+LetterB, never optimal in local alignment with gap penalties
		DPI(0, uPrefixLengthB) = MINUS_INFINITY;
		}

	SCORE scoreMax = MINUS_INFINITY;
	unsigned uPrefixLengthAMax = uInsane;
	unsigned uPrefixLengthBMax = uInsane;

// ============
// Main DP loop
// ============
	SCORE scoreGapCloseB = MINUS_INFINITY;
	for (unsigned uPrefixLengthB = 1; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
		const ProfPos &PPB = PB[uPrefixLengthB - 1];

		SCORE scoreGapCloseA = MINUS_INFINITY;
		for (unsigned uPrefixLengthA = 1; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
			{
			const ProfPos &PPA = PA[uPrefixLengthA - 1];

			{
		// Match M=LetterA+LetterB
			SCORE scoreLL = ScoreProfPos2(PPA, PPB);

			SCORE scoreMM = DPM(uPrefixLengthA-1, uPrefixLengthB-1);
			SCORE scoreDM = DPD(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseA;
			SCORE scoreIM = DPI(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseB;

			SCORE scoreBest;
			if (scoreMM >= scoreDM && scoreMM >= scoreIM)
				scoreBest = scoreMM;
			else if (scoreDM >= scoreMM && scoreDM >= scoreIM)
				scoreBest = scoreDM;
			else 
				{
				assert(scoreIM >= scoreMM && scoreIM >= scoreDM);
				scoreBest = scoreIM;
				}
			if (scoreBest < 0)
				scoreBest = 0;
			scoreBest += scoreLL;
			if (scoreBest > scoreMax)
				{
				scoreMax = scoreBest;
				uPrefixLengthAMax = uPrefixLengthA;
				uPrefixLengthBMax = uPrefixLengthB;
				}
			DPM(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

			{
		// Delete D=LetterA+GapB
			SCORE scoreMD = DPM(uPrefixLengthA-1, uPrefixLengthB) +
			  PA[uPrefixLengthA-1].m_scoreGapOpen;
			SCORE scoreDD = DPD(uPrefixLengthA-1, uPrefixLengthB);

			SCORE scoreBest;
			if (scoreMD >= scoreDD)
				scoreBest = scoreMD;
			else
				{
				assert(scoreDD >= scoreMD);
				scoreBest = scoreDD;
				}
			DPD(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

		// Insert I=GapA+LetterB
			{
			SCORE scoreMI = DPM(uPrefixLengthA, uPrefixLengthB-1) +
			  PB[uPrefixLengthB - 1].m_scoreGapOpen;
			SCORE scoreII = DPI(uPrefixLengthA, uPrefixLengthB-1);

			SCORE scoreBest;
			if (scoreMI >= scoreII)
				scoreBest = scoreMI;
			else 
				{
				assert(scoreII > scoreMI);
				scoreBest = scoreII;
				}
			DPI(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

			scoreGapCloseA = PPA.m_scoreGapClose;
			}
		scoreGapCloseB = PPB.m_scoreGapClose;
		}

#if TRACE
	Log("DPM:\n");
	ListDP(DPM_, PA, PB, uPrefixLengthA, uPrefixLengthB);
	Log("DPD:\n");
	ListDP(DPD_, PA, PB, uPrefixLengthA, uPrefixLengthB);
	Log("DPI:\n");
	ListDP(DPI_, PA, PB, uPrefixLengthA, uPrefixLengthB);
#endif

	assert(scoreMax == DPM(uPrefixLengthAMax, uPrefixLengthBMax));
	TraceBackSW(PA, uLengthA, PB, uLengthB, DPM_, DPD_, DPI_, 
	  uPrefixLengthAMax, uPrefixLengthBMax, Path);

#if	TRACE
	SCORE scorePath = FastScorePath2(PA, uLengthA, PB, uLengthB, Path);
	Path.LogMe();
	Log("Score = %s Path = %s\n", LocalScoreToStr(scoreMax), LocalScoreToStr(scorePath));
#endif

	delete[] DPM_;
	delete[] DPD_;
	delete[] DPI_;

	return scoreMax;
	}