C++ (Cpp) MSA::GuessAlphaの例

コード例 #1

ファイル: profile.cpp プロジェクト: Wyss/mauve-py

void SetProfileProfileAlphabet(MSA &msa1, MSA &msa2)
{
	ALPHA Alpha = ALPHA_Undefined;
	switch (g_SeqType.get())
		{
	case SEQTYPE_Auto:
		Alpha = msa1.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 SeqType");
		}
	SetAlpha(Alpha);

	msa1.FixAlpha();
	msa2.FixAlpha();

	if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
		SetPPScore(PPSCORE_SPN);
}

コード例 #2

ファイル: dosp.cpp プロジェクト: ggrekhov/ugene

void DoSP()
	{
    MuscleContext *ctx = getMuscleContext();

	TextFile f(ctx->params.g_pstrSPFileName);

	MSA a;
	a.FromFile(f);

	ALPHA Alpha = ALPHA_Undefined;
	switch (ctx->params.g_SeqType)
		{
	case SEQTYPE_Auto:
		Alpha = a.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 SeqType");
		}
	SetAlpha(Alpha);
	a.FixAlpha();

	SetPPScore();

	const unsigned uSeqCount = a.GetSeqCount();
	if (0 == uSeqCount)
		Quit("No sequences in input file %s", ctx->params.g_pstrSPFileName);

	MSA::SetIdCount(uSeqCount);
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		a.SetSeqId(uSeqIndex, uSeqIndex);

	SetSeqWeightMethod(ctx->params.g_SeqWeight1);
	Tree tree;
	TreeFromMSA(a, tree, ctx->params.g_Cluster2, ctx->params.g_Distance2, ctx->params.g_Root2);
	SetMuscleTree(tree);
	SetMSAWeightsMuscle((MSA &) a);

	SCORE SP = ObjScoreSP(a);

	Log("File=%s;SP=%.4g\n", ctx->params.g_pstrSPFileName, SP);
	fprintf(stderr, "File=%s;SP=%.4g\n", ctx->params.g_pstrSPFileName, SP);
	}

コード例 #3

ファイル: refine.cpp プロジェクト: Wyss/mauve-py

void Refine()
	{
	SetOutputFileName(g_pstrOutFileName.get());
	SetInputFileName(g_pstrInFileName.get());
	SetStartTime();

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

	TextFile fileIn(g_pstrInFileName.get());
	MSA msa;
	msa.FromFile(fileIn);

	const unsigned uSeqCount = msa.GetSeqCount();
	if (0 == uSeqCount)
		Quit("No sequences in input file");

	ALPHA Alpha = ALPHA_Undefined;
	switch (g_SeqType.get())
		{
	case SEQTYPE_Auto:
		Alpha = msa.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 SeqType");
		}
	SetAlpha(Alpha);
	msa.FixAlpha();

	SetPPScore();
	if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
		SetPPScore(PPSCORE_SPN);

	MSA::SetIdCount(uSeqCount);

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

	Tree GuideTree;
	TreeFromMSA(msa, GuideTree, g_Cluster2.get(), g_Distance2.get(), g_Root2.get());
	SetMuscleTree(GuideTree);

	if (g_bAnchors.get())
		RefineVert(msa, GuideTree, g_uMaxIters.get());
	else
		RefineHoriz(msa, GuideTree, g_uMaxIters.get(), false, false);

	ValidateMuscleIds(msa);
	ValidateMuscleIds(GuideTree);

//	TextFile fileOut(g_pstrOutFileName.get(), true);
//	msa.ToFile(fileOut);
	MuscleOutput(msa);
	}

コード例 #4

ファイル: refinew.cpp プロジェクト: bigmuscle/bigmuscle

void DoRefineW()
	{
	SetOutputFileName(g_pstrOutFileName);
	SetInputFileName(g_pstrInFileName);
	SetStartTime();

	SetMaxIters(g_uMaxIters);
	SetSeqWeightMethod(g_SeqWeight1);

	TextFile fileIn(g_pstrInFileName);
	MSA msa;
	msa.FromFile(fileIn);

	const unsigned uSeqCount = msa.GetSeqCount();
	if (0 == uSeqCount)
		Quit("No sequences in input file");

	MSA::SetIdCount(uSeqCount);

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

	ALPHA Alpha = ALPHA_Undefined;
	switch (g_SeqType)
		{
	case SEQTYPE_Auto:
		Alpha = msa.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 SeqType");
		}
	SetAlpha(Alpha);
	msa.FixAlpha();

	if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
		SetPPScore(PPSCORE_SPN);

	MSA msaOut;
	RefineW(msa, msaOut);

//	ValidateMuscleIds(msa);

//	TextFile fileOut(g_pstrOutFileName, true);
//	msaOut.ToFile(fileOut);
	MuscleOutput(msaOut);
	}