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C++ SeqVect::ToFile方法代码示例

本文整理汇总了C++中SeqVect::ToFile方法的典型用法代码示例。如果您正苦于以下问题：C++ SeqVect::ToFile方法的具体用法？C++ SeqVect::ToFile怎么用？C++ SeqVect::ToFile使用的例子？那么恭喜您, 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SeqVect的用法示例。


在下文中一共展示了SeqVect::ToFile方法的4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: DoMuscle

void DoMuscle()
	{
	SetOutputFileName(g_pstrOutFileName.get());
	SetInputFileName(g_pstrInFileName.get());

	SetMaxIters(g_uMaxIters.get());
	SetSeqWeightMethod(g_SeqWeight1.get());

	TextFile fileIn(g_pstrInFileName.get());
	SeqVect v;
	v.FromFASTAFile(fileIn);
	const unsigned uSeqCount = v.Length();

	if (0 == uSeqCount)
		Quit("No sequences in input file");

	ALPHA Alpha = ALPHA_Undefined;
	switch (g_SeqType.get())
		{
	case SEQTYPE_Auto:
		Alpha = v.GuessAlpha();
		break;

	case SEQTYPE_Protein:
		Alpha = ALPHA_Amino;
		break;

	case SEQTYPE_DNA:
		Alpha = ALPHA_DNA;
		break;

	case SEQTYPE_RNA:
		Alpha = ALPHA_RNA;
		break;

	default:
		Quit("Invalid seq type");
		}
	SetAlpha(Alpha);
	v.FixAlpha();

//
// AED 21/12/06: Moved matrix loading code inside the PP param function so it gets called for all alignment types
//
	SetPPScore();


	unsigned uMaxL = 0;
	unsigned uTotL = 0;
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		unsigned L = v.GetSeq(uSeqIndex).Length();
		uTotL += L;
		if (L > uMaxL)
			uMaxL = L;
		}

	SetIter(1);
	g_bDiags.get() = g_bDiags1.get();
	SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount);

	SetMuscleSeqVect(v);

	MSA::SetIdCount(uSeqCount);

// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		v.SetSeqId(uSeqIndex, uSeqIndex);

	if (0 == uSeqCount)
		Quit("Input file '%s' has no sequences", g_pstrInFileName.get());
	if (1 == uSeqCount)
		{
		TextFile fileOut(g_pstrOutFileName.get(), true);
		v.ToFile(fileOut);
		return;
		}

	if (uSeqCount > 1)
		MHackStart(v);

// First iteration
	Tree GuideTree;
	if (0 != g_pstrUseTreeFileName.get())
		{
	// Discourage users...
		if (!g_bUseTreeNoWarn.get())
			fprintf(stderr, g_strUseTreeWarning);

	// Read tree from file
		TextFile TreeFile(g_pstrUseTreeFileName.get());
		GuideTree.FromFile(TreeFile);

	// Make sure tree is rooted
		if (!GuideTree.IsRooted())
			Quit("User tree must be rooted");

		if (GuideTree.GetLeafCount() != uSeqCount)
			Quit("User tree does not match input sequences");
//.........这里部分代码省略.........
开发者ID:Wyss，项目名称:mauve-py，代码行数:101，代码来源:domuscle.cpp

示例2: RefineW


//.........这里部分代码省略.........
		}
		std::vector< unsigned > seqid_map( vr.size() );
		for( size_t seqI = 0; seqI < vr.size(); ++seqI )
		{
			seqid_map[seqI] = vr[seqI]->GetId();
			vr[seqI]->SetId(seqI);
		}

		MSA msaTmp;
		if( vr.size() > 1 )
			MUSCLE(vr, msaTmp);

		// remap the seqids to their original state
		for( size_t seqI = 0; seqI < vr.size(); ++seqI )
			vr[seqI]->SetId(seqid_map[seqI]);

		// merge empty seqs back in
		{
			const unsigned uSeqCount = msaOut.GetSeqCount();

			const unsigned uColCount1 = msaOut.GetColCount();
			const unsigned uColCount2 = vr.size() > 1 ? msaTmp.GetColCount() : vr[0]->size();
			const unsigned uColCountCat = uColCount1 + uColCount2;
			for( unsigned seqI = 0; seqI < vr.size(); ++seqI )
			{
				unsigned uSeqIndex = msaOut.GetSeqIndex(seqid_map[seqI]);
				if( vr.size() > 1 )
				{
					unsigned uSeqIndex2 = msaTmp.GetSeqIndex(seqI);
					for (unsigned uColIndex = 0; uColIndex < uColCount2; ++uColIndex)
					{
						const char c = msaTmp.GetChar(uSeqIndex2, uColIndex);
						msaOut.SetChar(uSeqIndex, uColCount1 + uColIndex, c);
					}
				}else{
					for (unsigned uColIndex = 0; uColIndex < uColCount2; ++uColIndex)
					{
						const char c = vr[0]->GetChar(uColIndex);
						msaOut.SetChar(uSeqIndex, uColCount1 + uColIndex, c);
					}
				}
			}
			for( unsigned seqI = 0; seqI < empty_seqs.size(); ++seqI )
			{
				unsigned uSeqId2 = v[empty_seqs[seqI]]->GetId();
				unsigned uSeqIndex = msaOut.GetSeqIndex(uSeqId2);
				for (unsigned uColIndex = 0; uColIndex < uColCount2; ++uColIndex)
				{
					msaOut.SetChar(uSeqIndex, uColCount1 + uColIndex, '-');
				}
			}
			vr.clear();
		}
//		AppendMSA(msaOut, msaTmp);
		// end AED 5/20/06

		if (uWindowIndex == g_uSaveWindow.get())
			{
			MSA msaInTmp;
			unsigned uOutCols = msaOut.GetColCount();
			unsigned un = uColTo - uColFrom + 1;
			MSAFromColRange(msaIn, uColFrom, un, msaInTmp);

			char fn[256];
			sprintf(fn, "win%d_inaln.tmp", uWindowIndex);
			TextFile fIn(fn, true);
			msaInTmp.ToFile(fIn);

			sprintf(fn, "win%d_inseqs.tmp", uWindowIndex);
			TextFile fv(fn, true);
			v.ToFile(fv);

			sprintf(fn, "win%d_outaln.tmp", uWindowIndex);
			TextFile fOut(fn, true);
			msaTmp.ToFile(fOut);
			}

#if	MEMDEBUG
		void FreeDPMemSPN();
		FreeDPMemSPN();

		_CrtMemState s2;
		_CrtMemCheckpoint(&s2);

		_CrtMemState s;
		_CrtMemDifference(&s, &s1, &s2);

		_CrtMemDumpStatistics(&s);
		_CrtMemDumpAllObjectsSince(&s1);
		exit(1);
#endif
//#if	DEBUG
//		AssertMSAEqIgnoreCaseAndGaps(msaInTmp, msaTmp);
//#endif
		}
	if (!g_bQuiet.get())
		fprintf(stderr, "\n");

//	AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);//@@uncomment!
	}
开发者ID:Wyss，项目名称:mauve-py，代码行数:101，代码来源:refinew.cpp

示例3: DoMuscle

void DoMuscle(CompositeVect*CVLocation)
	{
	SetOutputFileName(g_pstrOutFileName);
	SetInputFileName(g_pstrInFileName);

	SetMaxIters(g_uMaxIters);
	SetSeqWeightMethod(g_SeqWeight1);

	TextFile fileIn(g_pstrInFileName);
	SeqVect v;
	v.FromFASTAFile(fileIn);
	const unsigned uSeqCount = v.Length();

	if (0 == uSeqCount)
		Quit("No sequences in input file");

	ALPHA Alpha = ALPHA_Undefined;
	switch (g_SeqType)
		{
	case SEQTYPE_Auto:
		Alpha = v.GuessAlpha();
		break;

	case SEQTYPE_Protein:
		Alpha = ALPHA_Amino;
		break;

	case SEQTYPE_DNA:
		Alpha = ALPHA_DNA;
		break;

	case SEQTYPE_RNA:
		Alpha = ALPHA_RNA;
		break;

	default:
		Quit("Invalid seq type");
		}
	SetAlpha(Alpha);
	v.FixAlpha();

	PTR_SCOREMATRIX UserMatrix = 0;
	if (0 != g_pstrMatrixFileName)
		{
		const char *FileName = g_pstrMatrixFileName;
		const char *Path = getenv("MUSCLE_MXPATH");
		if (Path != 0)
			{
			size_t n = strlen(Path) + 1 + strlen(FileName) + 1;
			char *NewFileName = new char[n];
			sprintf(NewFileName, "%s/%s", Path, FileName);
			FileName = NewFileName;
			}
		TextFile File(FileName);
		UserMatrix = ReadMx(File);
		g_Alpha = ALPHA_Amino;
		g_PPScore = PPSCORE_SP;
		}

	SetPPScore();

	if (0 != UserMatrix)
		g_ptrScoreMatrix = UserMatrix;

	unsigned uMaxL = 0;
	unsigned uTotL = 0;
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		unsigned L = v.GetSeq(uSeqIndex).Length();
		uTotL += L;
		if (L > uMaxL)
			uMaxL = L;
		}

	SetIter(1);
	g_bDiags = g_bDiags1;
	SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount);

	SetMuscleSeqVect(v);

	MSA::SetIdCount(uSeqCount);

// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		v.SetSeqId(uSeqIndex, uSeqIndex);

	if (0 == uSeqCount)
		Quit("Input file '%s' has no sequences", g_pstrInFileName);
	if (1 == uSeqCount)
		{
		TextFile fileOut(g_pstrOutFileName, true);
		v.ToFile(fileOut);
		return;
		}

	if (uSeqCount > 1)
		MHackStart(v);

// First iteration
//.........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:domuscle.cpp

示例4: RefineW

void RefineW(const MSA &msaIn, MSA &msaOut)
	{
	const unsigned uSeqCount = msaIn.GetSeqCount();
	const unsigned uColCount = msaIn.GetColCount();

// Reserve same nr seqs, 20% more cols
	const unsigned uReserveColCount = (uColCount*120)/100;
	msaOut.SetSize(uSeqCount, uReserveColCount);

	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		msaOut.SetSeqName(uSeqIndex, msaIn.GetSeqName(uSeqIndex));
		msaOut.SetSeqId(uSeqIndex, msaIn.GetSeqId(uSeqIndex));
		}

	const unsigned uWindowCount = (uColCount + g_uRefineWindow - 1)/g_uRefineWindow;
	if (0 == g_uWindowTo)
		g_uWindowTo = uWindowCount - 1;

#if	MEMDEBUG
	_CrtSetBreakAlloc(1560);
#endif

	if (g_uWindowOffset > 0)
		{
		MSA msaTmp;
		MSAFromColRange(msaIn, 0, g_uWindowOffset, msaOut);
		}

	fprintf(stderr, "\n");
	for (unsigned uWindowIndex = g_uWindowFrom; uWindowIndex <= g_uWindowTo; ++uWindowIndex)
		{
		fprintf(stderr, "Window %d of %d    \r", uWindowIndex, uWindowCount);
		const unsigned uColFrom = g_uWindowOffset + uWindowIndex*g_uRefineWindow;
		unsigned uColTo = uColFrom + g_uRefineWindow - 1;
		if (uColTo >= uColCount)
			uColTo = uColCount - 1;
		assert(uColTo >= uColFrom);

		SeqVect v;
		SeqVectFromMSACols(msaIn, uColFrom, uColTo, v);

#if	MEMDEBUG
		_CrtMemState s1;
		_CrtMemCheckpoint(&s1);
#endif

		MSA msaTmp;
		MUSCLE(v, msaTmp);
		AppendMSA(msaOut, msaTmp);
		if (uWindowIndex == g_uSaveWindow)
			{
			MSA msaInTmp;
			unsigned uOutCols = msaOut.GetColCount();
			unsigned un = uColTo - uColFrom + 1;
			MSAFromColRange(msaIn, uColFrom, un, msaInTmp);

			char fn[256];
			sprintf(fn, "win%d_inaln.tmp", uWindowIndex);
			TextFile fIn(fn, true);
			msaInTmp.ToFile(fIn);

			sprintf(fn, "win%d_inseqs.tmp", uWindowIndex);
			TextFile fv(fn, true);
			v.ToFile(fv);

			sprintf(fn, "win%d_outaln.tmp", uWindowIndex);
			TextFile fOut(fn, true);
			msaTmp.ToFile(fOut);
			}

#if	MEMDEBUG
		void FreeDPMemSPN();
		FreeDPMemSPN();

		_CrtMemState s2;
		_CrtMemCheckpoint(&s2);

		_CrtMemState s;
		_CrtMemDifference(&s, &s1, &s2);

		_CrtMemDumpStatistics(&s);
		_CrtMemDumpAllObjectsSince(&s1);
		exit(1);
#endif
//#if	DEBUG
//		AssertMSAEqIgnoreCaseAndGaps(msaInTmp, msaTmp);
//#endif
		}
	fprintf(stderr, "\n");

//	AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);//@@uncomment!
	}
开发者ID:bigmuscle，项目名称:bigmuscle，代码行数:93，代码来源:refinew.cpp


注：本文中的SeqVect::ToFile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。