C++ SeqVect::GetSeq方法代码示例

void DistPWScoreDist(const SeqVect &v, DistFunc &DF)
	{
	SEQWEIGHT SeqWeightSave = GetSeqWeightMethod();
	SetSeqWeightMethod(SEQWEIGHT_Henikoff);

	const unsigned uSeqCount = v.Length();
	DF.SetCount(uSeqCount);

	const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2;
	unsigned uCount = 0;
	SetProgressDesc("PW ScoreDist");
	for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
		{
		const Seq &s1 = v.GetSeq(uSeqIndex1);
		MSA msa1;
		msa1.FromSeq(s1);
		for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqIndex1; ++uSeqIndex2)
			{
			if (0 == uCount%20)
				Progress(uCount, uPairCount);
			++uCount;
			const Seq &s2 = v.GetSeq(uSeqIndex2);
			MSA msa2;
			msa2.FromSeq(s2);
		
			PWPath Path;
			MSA msaOut;
			AlignTwoMSAs(msa1, msa2, msaOut, Path, false, false);

			float d = (float) GetScoreDist(msaOut, 0, 1);
			DF.SetDist(uSeqIndex1, uSeqIndex2, d);
			}
		}
	ProgressStepsDone();

	SetSeqWeightMethod(SeqWeightSave);
	}

void MHackStart(SeqVect &v)
	{
	if (ALPHA_Amino != g_Alpha)
		return;

	const unsigned uSeqCount = v.Length();
	M = new bool[uSeqCount];
	memset(M, 0, uSeqCount*sizeof(bool));
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		Seq &s = v.GetSeq(uSeqIndex);
		if (0 == s.Length())
			continue;
		unsigned uId = s.GetId();
		if (s[0] == 'M' || s[0] == 'm')
			{
			M[uId] = true;
			s[0] = 'X';
			}
		}
	}

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.........

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.........

void ProgAlignSubFams()
	{
	MSA msaOut;

	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();

	PTR_SCOREMATRIX UserMatrix = 0;
	if (0 != g_pstrMatrixFileName.get())
		{
		const char *FileName = g_pstrMatrixFileName.get();
		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;

	if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
		{
		SetPPScore(PPSCORE_SPN);
		g_Distance1.get() = DISTANCE_Kmer4_6;
		}

	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 (uSeqCount > 1)
		MHackStart(v);

	if (0 == uSeqCount)
		{
//.........这里部分代码省略.........