params.cpp

unix,linux下编译。用于蛋白质

	g_bNormalizeCounts = false;

	g_dSmoothScoreCeil = 999.0;		// disable
	g_dMinBestColScore = 90;
	g_dMinSmoothScore = 90;

	g_Distance1 = DISTANCE_Kmer4_6;
	g_Distance2 = DISTANCE_PctIdKimura;
	}

static void FlagParam(const char *OptName, bool *ptrParam, bool bValueIfFlagSet)
	{
	bool bIsSet = FlagOpt(OptName);
	if (bIsSet)
		*ptrParam = bValueIfFlagSet;
	}

static void StrParam(const char *OptName, const char **ptrptrParam)
	{
	const char *opt = ValueOpt(OptName);
	if (0 != opt)
		*ptrptrParam = opt;
	}

static void FloatParam(const char *OptName, float *ptrParam)
	{
	const char *opt = ValueOpt(OptName);
	if (0 != opt)
		*ptrParam = (float) atof(opt);
	}

static void UintParam(const char *OptName, unsigned *ptrParam)
	{
	const char *opt = ValueOpt(OptName);
	if (0 != opt)
		*ptrParam = atou(opt);
	}

static void EnumParam(const char *OptName, EnumOpt *Opts, int *Param)
	{
	const char *Value = ValueOpt(OptName);
	if (0 == Value)
		return;

	for (;;)
		{
		if (0 == Opts->pstrOpt)
			Quit("Invalid parameter -%s %s", OptName, Value);
		if (0 == stricmp(Value, Opts->pstrOpt))
			{
			*Param = Opts->iValue;
			return;
			}
		++Opts;
		}
	}

static void SetPPDefaultParams()
	{
	switch (g_PPScore)
		{
	case PPSCORE_SP:
		SetDefaultsSP();
		break;

	case PPSCORE_LE:
		SetDefaultsLE();
		break;

	case PPSCORE_SV:
		SetDefaultsSV();
		break;

	case PPSCORE_SPN:
		switch (g_Alpha)
			{
		case ALPHA_DNA:
			SetDefaultsSPN_DNA();
			break;
		case ALPHA_RNA:
			SetDefaultsSPN_RNA();
			break;
		default:
			Quit("Invalid alpha %d", g_Alpha);
			}
		break;

	default:
		Quit("Invalid g_PPScore");
		}
	}

static void SetPPCommandLineParams()
	{
	FloatParam("GapOpen", &g_scoreGapOpen);
	FloatParam("GapOpen2", &g_scoreGapOpen2);
	FloatParam("GapExtend", &g_scoreGapExtend);
	FloatParam("GapExtend2", &g_scoreGapExtend2);
	FloatParam("GapAmbig", &g_scoreAmbigFactor);
	FloatParam("Center", &g_scoreCenter);
	FloatParam("SmoothScoreCeil", &g_dSmoothScoreCeil);
	FloatParam("MinBestColScore", &g_dMinBestColScore);
	FloatParam("MinSmoothScore", &g_dMinSmoothScore);

	EnumParam("Distance", DISTANCE_Opts, (int *) &g_Distance1);
	EnumParam("Distance", DISTANCE_Opts, (int *) &g_Distance2);

	EnumParam("Distance1", DISTANCE_Opts, (int *) &g_Distance1);
	EnumParam("Distance2", DISTANCE_Opts, (int *) &g_Distance2);
	}

void SetPPScore(bool bRespectFlagOpts)
	{
	if (bRespectFlagOpts)
		{
		if (FlagOpt("SP"))
			g_PPScore = PPSCORE_SP;
		else if (FlagOpt("LE"))
			g_PPScore = PPSCORE_LE;
		else if (FlagOpt("SV"))
			g_PPScore = PPSCORE_SV;
		else if (FlagOpt("SPN"))
			g_PPScore = PPSCORE_SPN;
		}

	switch (g_PPScore)
		{
	case PPSCORE_LE:
	case PPSCORE_SP:
	case PPSCORE_SV:
		if (ALPHA_RNA == g_Alpha || ALPHA_DNA == g_Alpha)
			g_PPScore = PPSCORE_SPN;
		break;
	case PPSCORE_SPN:
		if (ALPHA_Amino == g_Alpha)
			g_PPScore = PPSCORE_LE;
		break;
		}

	SetPPDefaultParams();
	SetPPCommandLineParams();

	if (g_bVerbose)
		ListParams();
	}

void SetPPScore(PPSCORE p)
	{
	g_PPScore = p;
	SetPPScore(true);
	}

static void SetMaxSecs()
	{
	float fMaxHours = 0.0;
	FloatParam("MaxHours", &fMaxHours);
	if (0.0 == fMaxHours)
		return;
	g_ulMaxSecs = (unsigned long) (fMaxHours*60*60);
	}

static bool CanDoLowComplexity()
	{
	if (g_SeqWeight1 != SEQWEIGHT_ClustalW)
		return false;
	if (1 == g_uMaxIters)
		return true;
	return g_SeqWeight2 == SEQWEIGHT_ClustalW;
	}

bool MissingCommand()
	{
	if (strcmp(g_pstrInFileName, "-"))
		return false;
	if (0 != g_pstrFileName1)
		return false;
	if (0 != g_pstrSPFileName)
		return false;
	return true;
	}

void SetParams()
	{
	SetMaxSecs();

	StrParam("in", &g_pstrInFileName);
	StrParam("out", &g_pstrOutFileName);

	StrParam("FASTAOut", &g_pstrFASTAOutFileName);
	StrParam("ClwOut", &g_pstrClwOutFileName);
	StrParam("ClwStrictOut", &g_pstrClwStrictOutFileName);
	StrParam("HTMLOut", &g_pstrHTMLOutFileName);
	StrParam("PHYIOut", &g_pstrPHYIOutFileName);
	StrParam("PHYSOut", &g_pstrPHYSOutFileName);
	StrParam("MSFOut", &g_pstrMSFOutFileName);

	StrParam("in1", &g_pstrFileName1);
	StrParam("in2", &g_pstrFileName2);

	StrParam("Matrix", &g_pstrMatrixFileName);
	StrParam("SPScore", &g_pstrSPFileName);

	StrParam("UseTree_NoWarn", &g_pstrUseTreeFileName);
	if (0 != g_pstrUseTreeFileName)
		g_bUseTreeNoWarn = true;

	StrParam("UseTree", &g_pstrUseTreeFileName);
	StrParam("ComputeWeights", &g_pstrComputeWeightsFileName);
	StrParam("ScoreFile", &g_pstrScoreFileName);
	StrParam("DistMx1", &g_pstrDistMxFileName1);
	StrParam("DistMx2", &g_pstrDistMxFileName2);

	FlagParam("Core", &g_bCatchExceptions, false);
	FlagParam("NoCore", &g_bCatchExceptions, true);

	FlagParam("Diags1", &g_bDiags1, true);
	FlagParam("Diags2", &g_bDiags2, true);

	bool Diags = false;
	FlagParam("Diags", &Diags, true);
	if (Diags)
		{
		g_bDiags1 = true;
		g_bDiags2 = true;
		}

	FlagParam("Anchors", &g_bAnchors, true);
	FlagParam("NoAnchors", &g_bAnchors, false);

	FlagParam("Quiet", &g_bQuiet, true);
	FlagParam("Verbose", &g_bVerbose, true);
	FlagParam("Version", &g_bVersion, true);
	FlagParam("Stable", &g_bStable, true);
	FlagParam("Group", &g_bStable, false);
	FlagParam("Refine", &g_bRefine, true);
	FlagParam("RefineW", &g_bRefineW, true);
	FlagParam("ProfDB", &g_bProfDB, true);
	FlagParam("SW", &g_bSW, true);
	FlagParam("ClusterOnly", &g_bClusterOnly, true);
	FlagParam("Profile", &g_bProfile, true);
	FlagParam("PPScore", &g_bPPScore, true);
	FlagParam("Brenner", &g_bBrenner, true);
	FlagParam("Dimer", &g_bDimer, true);

	FlagParam("MSF", &g_bMSF, true);
	FlagParam("PHYI", &g_bPHYI, true);
	FlagParam("PHYS", &g_bPHYS, true);
	FlagParam("clw", &g_bAln, true);
	FlagParam("HTML", &g_bHTML, true);
	FlagParam("FASTA", &g_bFASTA, true);
	FlagParam("PAS", &g_bPAS, true);
	FlagParam("MakeTree", &g_bMakeTree, true);

	bool b = false;
	FlagParam("clwstrict", &b, true);
	if (b)
		{
		g_bAln = true;
		g_bClwStrict = true;
		}

	UintParam("MaxIters", &g_uMaxIters);
	UintParam("MaxTrees", &g_uMaxTreeRefineIters);
	UintParam("SmoothWindow", &g_uSmoothWindowLength);
	UintParam("RefineWindow", &g_uRefineWindow);
	UintParam("FromWindow", &g_uWindowFrom);
	UintParam("ToWindow", &g_uWindowTo);
	UintParam("SaveWindow", &g_uSaveWindow);
	UintParam("WindowOffset", &g_uWindowOffset);
	UintParam("AnchorSpacing", &g_uAnchorSpacing);
	UintParam("DiagLength", &g_uMinDiagLength);
	UintParam("DiagMargin", &g_uDiagMargin);
	UintParam("DiagBreak", &g_uMaxDiagBreak);
	UintParam("MaxSubFam", &g_uMaxSubFamCount);

	UintParam("Hydro", &g_uHydrophobicRunLength);
	FlagParam("TomHydro", &g_bTomHydro, true);
	if (g_bTomHydro)
		g_uHydrophobicRunLength = 0;

	FloatParam("SUEFF", &g_dSUEFF);
	FloatParam("HydroFactor", &g_dHydroFactor);

	EnumParam("ObjScore", OBJSCORE_Opts, (int *) &g_ObjScore);
	EnumParam("TermGaps", TERMGAPS_Opts, (int *) &g_TermGaps);

	EnumParam("Weight", SEQWEIGHT_Opts, (int *) &g_SeqWeight1);
	EnumParam("Weight", SEQWEIGHT_Opts, (int *) &g_SeqWeight2);

	EnumParam("Weight1", SEQWEIGHT_Opts, (int *) &g_SeqWeight1);
	EnumParam("Weight2", SEQWEIGHT_Opts, (int *) &g_SeqWeight2);

	EnumParam("Cluster", CLUSTER_Opts, (int *) &g_Cluster1);
	EnumParam("Cluster", CLUSTER_Opts, (int *) &g_Cluster2);

	EnumParam("Cluster1", CLUSTER_Opts, (int *) &g_Cluster1);
	EnumParam("Cluster2", CLUSTER_Opts, (int *) &g_Cluster2);

	EnumParam("Root1", ROOT_Opts, (int *) &g_Root1);
	EnumParam("Root2", ROOT_Opts, (int *) &g_Root2);

	EnumParam("SeqType", SEQTYPE_Opts, (int *) &g_SeqType);

	g_scoreGapAmbig = g_scoreGapOpen*g_scoreAmbigFactor;
	g_bLow = CanDoLowComplexity();

	if (g_bDimer)
		g_bPrecompiledCenter = false;

	UintParam("MaxMB", &g_uMaxMB);
	if (0 == ValueOpt("MaxMB"))
		g_uMaxMB = (unsigned) (GetRAMSizeMB()*DEFAULT_MAX_MB_FRACT);
	}