C++ (Cpp) GlobalAlignNoDiags示例

示例#1

文件： glbalign.cpp 项目： Unode/ext_apps

SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
#if	TIMING
	TICKS t1 = GetClockTicks();
#endif
	if (0 == uLengthA)
		{
		AllInserts(Path, uLengthB);
		return 0;
		}
	else if (0 == uLengthB)
		{
		AllDeletes(Path, uLengthA);
		return 0;
		}

	SCORE Score = 0;
	if (g_bDiags)
		Score = GlobalAlignDiags(PA, uLengthA, PB, uLengthB, Path);
	else
		Score = GlobalAlignNoDiags(PA, uLengthA, PB, uLengthB, Path);
#if	TIMING
	TICKS t2 = GetClockTicks();
	g_ticksDP += (t2 - t1);
#endif
	return Score;
	}

示例#2

文件： gatest.cpp 项目： Unode/ext_apps

SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
	if (g_bDiags)
		return GlobalAlignDiags(PA, uLengthA, PB, uLengthB, Path);
	else
		return GlobalAlignNoDiags(PA, uLengthA, PB, uLengthB, Path);
	}

示例#3

文件： glbaligndiag.cpp 项目： bigmuscle/bigmuscle

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
		}

#if	TRACE
	{
	double dDPAreaWithoutDiags = uLengthA*uLengthB;
	Log("DP area with diags %.3g without %.3g pct saved %.3g %%\n",
	  dDPAreaWithDiags, dDPAreaWithoutDiags, (1.0 - dDPAreaWithDiags/dDPAreaWithoutDiags)*100.0);
	}
#endif
	g_dDPAreaWithDiags += dDPAreaWithDiags;
	return 0;
	}