C++ PWPath::LogMe方法代码示例

本文整理汇总了C++中PWPath::LogMe方法的典型用法代码示例。如果您正苦于以下问题：C++ PWPath::LogMe方法的具体用法？C++ PWPath::LogMe怎么用？C++ PWPath::LogMe使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类PWPath的用法示例。

在下文中一共展示了PWPath::LogMe方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: GlobalAlign

SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
#if	TIMING
	TICKS t1 = GetClockTicks();
#endif
	g_bKeepSimpleDP = true;
	PWPath SimplePath;
	GlobalAlignSimple(PA, uLengthA, PB, uLengthB, SimplePath);

	SCORE Score = NWSmall(PA, uLengthA, PB, uLengthB, Path);

	if (!Path.Equal(SimplePath))
		{
		Log("Simple:\n");
		SimplePath.LogMe();
		Log("Small:\n");
		Path.LogMe();
		Quit("Paths differ");
		}

#if	TIMING
	TICKS t2 = GetClockTicks();
	g_ticksDP += (t2 - t1);
#endif
	return Score;
	}

开发者ID:Unode，项目名称:ext_apps，代码行数:27，代码来源:glbalign.cpp

示例2: NWDASimple


//.........这里部分代码省略.........

#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;
	}

开发者ID:Wyss，项目名称:mauve-py，代码行数:101，代码来源:nwdasimple.cpp

示例3: SPTest

void SPTest()
	{
	SetPPScore(PPSCORE_SV);

	SetListFileName("c:\\tmp\\muscle.log", false);

	TextFile file1("c:\\tmp\\msa1.afa");
	TextFile file2("c:\\tmp\\msa2.afa");

	MSA msa1;
	MSA msa2;

	msa1.FromFile(file1);
	msa2.FromFile(file2);

	Log("msa1=\n");
	msa1.LogMe();
	Log("msa2=\n");
	msa2.LogMe();

	const unsigned uColCount = msa1.GetColCount();
	if (msa2.GetColCount() != uColCount)
		Quit("Different lengths");

	const unsigned uSeqCount1 = msa1.GetSeqCount();
	const unsigned uSeqCount2 = msa2.GetSeqCount();
	const unsigned uSeqCount = uSeqCount1 + uSeqCount2;

	MSA::SetIdCount(uSeqCount);

	for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
		{
		msa1.SetSeqWeight(uSeqIndex1, 1.0);
		msa1.SetSeqId(uSeqIndex1, uSeqIndex1);
		}

	for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
		{
		msa2.SetSeqWeight(uSeqIndex2, 1.0);
		msa2.SetSeqId(uSeqIndex2, uSeqCount1 + uSeqIndex2);
		}

	MSA alnA;
	MSA alnB;

	char strPathA[1024];
	char strPathB[1024];
	MakePath(uColCount, INDELS, strPathA);
	MakePath(uColCount, INDELS, strPathB);

	PWPath PathA;
	PWPath PathB;
	PathA.FromStr(strPathA);
	PathB.FromStr(strPathB);

	Log("PathA=\n");
	PathA.LogMe();
	Log("PathB=\n");
	PathB.LogMe();

	AlignTwoMSAsGivenPath(PathA, msa1, msa2, alnA);
	AlignTwoMSAsGivenPath(PathB, msa1, msa2, alnB);

	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		alnA.SetSeqWeight(uSeqIndex, 1.0);
		alnB.SetSeqWeight(uSeqIndex, 1.0);
		}

	unsigned Seqs1[1024];
	unsigned Seqs2[1024];

	for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
		Seqs1[uSeqIndex1] = uSeqIndex1;

	for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
		Seqs2[uSeqIndex2] = uSeqCount1 + uSeqIndex2;

	MSA msaA1;
	MSA msaA2;
	MSA msaB1;
	MSA msaB2;
	MSAFromSeqSubset(alnA, Seqs1, uSeqCount1, msaA1);
	MSAFromSeqSubset(alnB, Seqs1, uSeqCount1, msaB1);
	MSAFromSeqSubset(alnA, Seqs2, uSeqCount2, msaA2);
	MSAFromSeqSubset(alnB, Seqs2, uSeqCount2, msaB2);

	for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
		{
		msaA1.SetSeqWeight(uSeqIndex1, 1.0);
		msaB1.SetSeqWeight(uSeqIndex1, 1.0);
		}

	for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
		{
		msaA2.SetSeqWeight(uSeqIndex2, 1.0);
		msaB2.SetSeqWeight(uSeqIndex2, 1.0);
		}

	Log("msaA1=\n");
//.........这里部分代码省略.........

开发者ID:bigmuscle，项目名称:bigmuscle，代码行数:101，代码来源:sptest.cpp

示例4: SW


//.........这里部分代码省略.........

		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;
	}

开发者ID:Unode，项目名称:ext_apps，代码行数:101，代码来源:sw.cpp

示例5: TraceBackDimer

static SCORE TraceBackDimer(  const SCORE *DPM_, const SCORE *DPD_, const SCORE *DPI_,
                              const char *TBM_, const char *TBD_, const char *TBI_,
                              unsigned uLengthA, unsigned uLengthB, PWPath &Path)
{
    const unsigned uPrefixCountA = uLengthA + 1;

    unsigned uPrefixLengthA = uLengthA;
    unsigned uPrefixLengthB = uLengthB;

    char cEdge = 'M';
    SCORE scoreMax = DPM(uLengthA, uLengthB);
    if (DPD(uLengthA, uLengthB) > scoreMax)
    {
        scoreMax = DPD(uLengthA, uLengthB);
        cEdge = 'D';
    }
    if (DPI(uLengthA, uLengthB) > scoreMax)
    {
        scoreMax = DPI(uLengthA, uLengthB);
        cEdge = 'I';
    }

    for (;;)
    {
        if (0 == uPrefixLengthA && 0 == uPrefixLengthB)
            break;

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

#if TRACE
        Log("PLA=%u PLB=%u Edge=%c\n", uPrefixLengthA, uPrefixLengthB, cEdge);
#endif
        switch (cEdge)
        {
        case 'M':
            assert(uPrefixLengthA > 0 && uPrefixLengthB > 0);
            cEdge = TBM(uPrefixLengthA, uPrefixLengthB);
            --uPrefixLengthA;
            --uPrefixLengthB;
            break;
        case 'D':
            assert(uPrefixLengthA > 0);
            cEdge = TBD(uPrefixLengthA, uPrefixLengthB);
            --uPrefixLengthA;
            break;
        case 'I':
            assert(uPrefixLengthB > 0);
            cEdge = TBI(uPrefixLengthA, uPrefixLengthB);
            --uPrefixLengthB;
            break;
        default:
            Quit("Invalid edge PLA=%u PLB=%u %c", uPrefixLengthA, uPrefixLengthB, cEdge);
        }
    }
#if	TRACE
    Path.LogMe();
#endif
    return scoreMax;
}

开发者ID:Unode，项目名称:ext_apps，代码行数:63，代码来源:glbalndimer.cpp

示例6: GlobalAlignDiags

SCORE GlobalAlignDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
#if	LIST_DIAGS
	TICKS t1 = GetClockTicks();
#endif

	DiagList DL;

	if (ALPHA_Amino == g_Alpha)
		FindDiags(PA, uLengthA, PB, uLengthB, DL);
	else if (ALPHA_DNA == g_Alpha || ALPHA_RNA == g_Alpha)
		FindDiagsNuc(PA, uLengthA, PB, uLengthB, DL);
	else
		Quit("GlobalAlignDiags: bad alpha");

#if	TRACE
	Log("GlobalAlignDiags, diag list:\n");
	DL.LogMe();
#endif

	DL.Sort();
	DL.DeleteIncompatible();

#if	TRACE
	Log("After DeleteIncompatible:\n");
	DL.LogMe();
#endif

	MergeDiags(DL);

#if	TRACE
	Log("After MergeDiags:\n");
	DL.LogMe();
#endif

	DPRegionList RL;
	DiagListToDPRegionList(DL, RL, uLengthA, uLengthB);

#if	TRACE
	Log("RegionList:\n");
	RL.LogMe();
#endif

#if	LIST_DIAGS
	{
	TICKS t2 = GetClockTicks();
	unsigned uArea = RL.GetDPArea();
	Log("ticks=%ld\n", (long) (t2 - t1));
	Log("area=%u\n", uArea);
	}
#endif

	g_dDPAreaWithoutDiags += uLengthA*uLengthB;

	double dDPAreaWithDiags = 0.0;
	const unsigned uRegionCount = RL.GetCount();
	for (unsigned uRegionIndex = 0; uRegionIndex < uRegionCount; ++uRegionIndex)
		{
		const DPRegion &r = RL.Get(uRegionIndex);

		PWPath RegPath;
		if (DPREGIONTYPE_Diag == r.m_Type)
			{
			DiagToPath(r.m_Diag, RegPath);
#if	TRACE_PATH
			Log("DiagToPath, path=\n");
			RegPath.LogMe();
#endif
			}
		else if (DPREGIONTYPE_Rect == r.m_Type)
			{
			const unsigned uRegStartPosA = r.m_Rect.m_uStartPosA;
			const unsigned uRegStartPosB = r.m_Rect.m_uStartPosB;
			const unsigned uRegLengthA = r.m_Rect.m_uLengthA;
			const unsigned uRegLengthB = r.m_Rect.m_uLengthB;
			const ProfPos *RegPA = PA + uRegStartPosA;
			const ProfPos *RegPB = PB + uRegStartPosB;

			dDPAreaWithDiags += uRegLengthA*uRegLengthB;
			GlobalAlignNoDiags(RegPA, uRegLengthA, RegPB, uRegLengthB, RegPath);
#if	TRACE_PATH
			Log("GlobalAlignNoDiags RegPath=\n");
			RegPath.LogMe();
#endif
			OffsetPath(RegPath, uRegStartPosA, uRegStartPosB);
#if	TRACE_PATH
			Log("After offset path, RegPath=\n");
			RegPath.LogMe();
#endif
			}
		else
			Quit("GlobalAlignDiags, Invalid region type %u", r.m_Type);

		AppendRegPath(Path, RegPath);
#if	TRACE_PATH
		Log("After AppendPath, path=");
		Path.LogMe();
#endif
		}
//.........这里部分代码省略.........

开发者ID:bigmuscle，项目名称:bigmuscle，代码行数:101，代码来源:glbaligndiag.cpp

注：本文中的PWPath::LogMe方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。