C++ TLS类代码示例

static const char *LocalScoreToStr(SCORE s)
	{
	static TLS<char[16]> str;
	if (s < -100000)
		return "     *";
	sprintf(str.get(), "%6.1f", s);
	return str.get();
	}

void SaveCurrentAlignment()
	{
    extern TLS<MSA *>ptrBestMSA;
	static TLS<bool> bCalled(false);
	if (bCalled.get())
		{
		fprintf(stderr,
		  "\nRecursive call to SaveCurrentAlignment, giving up attempt to save.\n");
		exit(EXIT_FatalError);
		}

	if (0 == ptrBestMSA.get())
		{
		fprintf(stderr, "\nAlignment not completed, cannot save.\n");
		Log("Alignment not completed, cannot save.\n");
		exit(EXIT_FatalError);
		}

	if (0 == pstrOutputFileName.get())
		{
		fprintf(stderr, "\nOutput file name not specified, cannot save.\n");
		exit(EXIT_FatalError);
		}

	fprintf(stderr, "\nSaving current alignment ...\n");

	TextFile fileOut(pstrOutputFileName.get(), true);
	ptrBestMSA.get()->ToFASTAFile(fileOut);

	fprintf(stderr, "Current alignment saved to \"%s\".\n", pstrOutputFileName.get());
	Log("Current alignment saved to \"%s\".\n", pstrOutputFileName.get());
	}

namespace muscle {


static TLS<const char *> pstrOutputFileName;

void SetOutputFileName(const char *out)
	{
	pstrOutputFileName.get() = out;
	}

void SetCurrentAlignment(MSA &msa)
	{
    extern TLS<MSA *>ptrBestMSA;
	ptrBestMSA.get() = &msa;
	}

void SaveCurrentAlignment()
	{
    extern TLS<MSA *>ptrBestMSA;
	static TLS<bool> bCalled(false);
	if (bCalled.get())
		{
		fprintf(stderr,
		  "\nRecursive call to SaveCurrentAlignment, giving up attempt to save.\n");
		exit(EXIT_FatalError);
		}

	if (0 == ptrBestMSA.get())
		{
		fprintf(stderr, "\nAlignment not completed, cannot save.\n");
		Log("Alignment not completed, cannot save.\n");
		exit(EXIT_FatalError);
		}

	if (0 == pstrOutputFileName.get())
		{
		fprintf(stderr, "\nOutput file name not specified, cannot save.\n");
		exit(EXIT_FatalError);
		}

	fprintf(stderr, "\nSaving current alignment ...\n");

	TextFile fileOut(pstrOutputFileName.get(), true);
	ptrBestMSA.get()->ToFASTAFile(fileOut);

	fprintf(stderr, "Current alignment saved to \"%s\".\n", pstrOutputFileName.get());
	Log("Current alignment saved to \"%s\".\n", pstrOutputFileName.get());
	}

void CheckMaxTime()
	{
	if (0 == g_ulMaxSecs.get())
		return;

	time_t Now = time(0);
	time_t ElapsedSecs = Now - GetStartTime();
	if (ElapsedSecs <= (time_t) g_ulMaxSecs.get())
		return;

	Log("Max time %s exceeded, elapsed seconds = %ul\n",
	  MaxSecsToStr(), ElapsedSecs);

	SaveCurrentAlignment();
	exit(EXIT_Success);
	}
} 

namespace muscle {

// UPGMA clustering in O(N^2) time and space.

#define	TRACE	0

#define	MIN(x, y)	((x) < (y) ? (x) : (y))
#define	MAX(x, y)	((x) > (y) ? (x) : (y))
#define	AVG(x, y)	(((x) + (y))/2)

static TLS<unsigned> g_uLeafCount;
static TLS<unsigned> g_uTriangleSize;
static TLS<unsigned> g_uInternalNodeCount;
static TLS<unsigned> g_uInternalNodeIndex;

// Triangular distance matrix is g_Dist.get(), which is allocated
// as a one-dimensional vector of length g_uTriangleSize.get().
// TriangleSubscript(i,j) maps row,column=i,j to the subscript
// into this vector.
// Row / column coordinates are a bit messy.
// Initially they are leaf indexes 0..N-1.
// But each time we create a new node (=new cluster, new subtree),
// we re-use one of the two rows that become available (the children
// of the new node). This saves memory.
// We keep track of this through the g_uNodeIndex.get() vector.
static TLS<dist_t *> g_Dist;

// Distance to nearest neighbor in row i of distance matrix.
// Subscript is distance matrix row.
static TLS<dist_t *> g_MinDist;

// Nearest neighbor to row i of distance matrix.
// Subscript is distance matrix row.
static TLS<unsigned *> g_uNearestNeighbor;

// Node index of row i in distance matrix.
// Node indexes are 0..N-1 for leaves, N..2N-2 for internal nodes.
// Subscript is distance matrix row.
static TLS<unsigned *> g_uNodeIndex;

// The following vectors are defined on internal nodes,
// subscripts are internal node index 0..N-2.
// For g_uLeft.get()/Right, value is the node index 0 .. 2N-2
// because a child can be internal or leaf.
static TLS<unsigned *> g_uLeft;
static TLS<unsigned *> g_uRight;
static TLS<dist_t *> g_Height;
static TLS<dist_t *> g_LeftLength;
static TLS<dist_t *> g_RightLength;

static inline unsigned TriangleSubscript(unsigned uIndex1, unsigned uIndex2)
	{
#if	DEBUG
	if (uIndex1 >= g_uLeafCount.get() || uIndex2 >= g_uLeafCount.get())
		Quit("TriangleSubscript(%u,%u) %u", uIndex1, uIndex2, g_uLeafCount.get());
#endif
	unsigned v;
	if (uIndex1 >= uIndex2)
		v = uIndex2 + (uIndex1*(uIndex1 - 1))/2;
	else
		v = uIndex1 + (uIndex2*(uIndex2 - 1))/2;
	assert(v < (g_uLeafCount.get()*(g_uLeafCount.get() - 1))/2);
	return v;
	}

static void ListState()
	{
	Log("Dist matrix\n");
	Log("     ");
	for (unsigned i = 0; i < g_uLeafCount.get(); ++i)
		{
		if (uInsane == g_uNodeIndex.get()[i])
			continue;
		Log("  %5u", g_uNodeIndex.get()[i]);
		}
	Log("\n");

	for (unsigned i = 0; i < g_uLeafCount.get(); ++i)
		{
		if (uInsane == g_uNodeIndex.get()[i])
			continue;
		Log("%5u  ", g_uNodeIndex.get()[i]);
		for (unsigned j = 0; j < g_uLeafCount.get(); ++j)
			{
			if (uInsane == g_uNodeIndex.get()[j])
				continue;
			if (i == j)
				Log("       ");
			else
				{
				unsigned v = TriangleSubscript(i, j);
				Log("%5.2g  ", g_Dist.get()[v]);
				}
			}
		Log("\n");
		}

	Log("\n");
	Log("    i   Node   NrNb      Dist\n");
	Log("-----  -----  -----  --------\n");
//.........这里部分代码省略.........

namespace muscle {

const unsigned TRIPLE_COUNT = 20*20*20;

struct TripleCount
	{
	unsigned m_uSeqCount;			// How many sequences have this triple?
	unsigned short *m_Counts;		// m_Counts[s] = nr of times triple found in seq s
	};
static TLS<TripleCount *> TripleCounts;

// WARNING: Sequences MUST be stripped of gaps and upper case!
void DistKmer20_3(const SeqVect &v, DistFunc &DF)
	{
	const unsigned uSeqCount = v.Length();

	DF.SetCount(uSeqCount);
	if (0 == uSeqCount)
		return;
	for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1)
		{
		DF.SetDist(uSeq1, uSeq1, 0);
		for (unsigned uSeq2 = 0; uSeq2 < uSeq1; ++uSeq2)
			DF.SetDist(uSeq1, uSeq2, 0);
		}

	const unsigned uTripleArrayBytes = TRIPLE_COUNT*sizeof(TripleCount);
	TripleCounts.get() = (TripleCount *) malloc(uTripleArrayBytes);
	if (0 == TripleCounts.get())
		Quit("Not enough memory (TripleCounts)");
	memset(TripleCounts.get(), 0, uTripleArrayBytes);

	for (unsigned uWord = 0; uWord < TRIPLE_COUNT; ++uWord)
		{
		TripleCount &tc = *(TripleCounts.get() + uWord);
		const unsigned uBytes = uSeqCount*sizeof(short);
		tc.m_Counts = (unsigned short *) malloc(uBytes);
		memset(tc.m_Counts, 0, uBytes);
		}

	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		Seq &s = *(v[uSeqIndex]);
		const unsigned uSeqLength = s.Length();
		for (unsigned uPos = 0; uPos < uSeqLength - 2; ++uPos)
			{
			const unsigned uLetter1 = CharToLetterEx(s[uPos]);
			if (uLetter1 >= 20)
				continue;
			const unsigned uLetter2 = CharToLetterEx(s[uPos+1]);
			if (uLetter2 >= 20)
				continue;
			const unsigned uLetter3 = CharToLetterEx(s[uPos+2]);
			if (uLetter3 >= 20)
				continue;

			const unsigned uWord = uLetter1 + uLetter2*20 + uLetter3*20*20;
			assert(uWord < TRIPLE_COUNT);

			TripleCount &tc = *(TripleCounts.get() + uWord);
			const unsigned uOldCount = tc.m_Counts[uSeqIndex];
			if (0 == uOldCount)
				++(tc.m_uSeqCount);

			++(tc.m_Counts[uSeqIndex]);
			}
		}

#if TRACE
	{
	Log("TripleCounts\n");
	unsigned uGrandTotal = 0;
	for (unsigned uWord = 0; uWord < TRIPLE_COUNT; ++uWord)
		{
		const TripleCount &tc = *(TripleCounts.get() + uWord);
		if (0 == tc.m_uSeqCount)
			continue;

		const unsigned uLetter3 = uWord/(20*20);
		const unsigned uLetter2 = (uWord - uLetter3*20*20)/20;
		const unsigned uLetter1 = uWord%20;
		Log("Word %6u %c%c%c   %6u",
		  uWord,
		  LetterToCharAmino(uLetter1),
		  LetterToCharAmino(uLetter2),
		  LetterToCharAmino(uLetter3),
		  tc.m_uSeqCount);

		unsigned uSeqCountWithThisWord = 0;
		for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
			{
			const unsigned uCount = tc.m_Counts[uSeqIndex];
			if (uCount > 0)
				{
				++uSeqCountWithThisWord;
				Log(" %u=%u", uSeqIndex, uCount);
				uGrandTotal += uCount;
				}
			}
		if (uSeqCountWithThisWord != tc.m_uSeqCount)
//.........这里部分代码省略.........

namespace muscle {

#if	DOUBLE_AFFINE

#define TRACE			0
#define TEST_SPFAST		0

static SCORE GapPenalty(unsigned uLength, bool Term, SCORE g, SCORE e)
	{
	//if (Term)
	//	{
	//	switch (g_TermGap)
	//		{
	//	case TERMGAP_Full:
	//		return g + (uLength - 1)*e;

	//	case TERMGAP_Half:
	//		return g/2 + (uLength - 1)*e;

	//	case TERMGAP_Ext:
	//		return uLength*e;
	//		}
	//	Quit("Bad termgap");
	//	}
	//else
	//	return g + (uLength - 1)*e;
	//return MINUS_INFINITY;
	return g + (uLength - 1)*e;
	}

static SCORE GapPenalty(unsigned uLength, bool Term)
	{
	SCORE s1 = GapPenalty(uLength, Term, g_scoreGapOpen.get(), g_scoreGapExtend.get());
#if	DOUBLE_AFFINE
	SCORE s2 = GapPenalty(uLength, Term, g_scoreGapOpen2.get(), g_scoreGapExtend2.get());
	if (s1 > s2)
		return s1;
	return s2;
#else
	return s1;
#endif
	}

static TLS<const MSA *> g_ptrMSA1;
static TLS<const MSA *> g_ptrMSA2;
static TLS<unsigned> g_uSeqIndex1;
static TLS<unsigned> g_uSeqIndex2;

static void LogGap(unsigned uStart, unsigned uEnd, unsigned uGapLength,
  bool bNTerm, bool bCTerm)
	{
	Log("%16.16s  ", "");
	for (unsigned i = 0; i < uStart; ++i)
		Log(" ");
	unsigned uMyLength = 0;
	for (unsigned i = uStart; i <= uEnd; ++i)
		{
		bool bGap1 = g_ptrMSA1.get()->IsGap(g_uSeqIndex1.get(), i);
		bool bGap2 = g_ptrMSA2.get()->IsGap(g_uSeqIndex2.get(), i);
		if (!bGap1 && !bGap2)
			Quit("Error -- neither gapping");
		if (bGap1 && bGap2)
			Log(".");
		else
			{
			++uMyLength;
			Log("-");
			}
		}
	SCORE s = GapPenalty(uGapLength, bNTerm || bCTerm);
	Log(" L=%d N%d C%d s=%.3g", uGapLength, bNTerm, bCTerm, s);
	Log("\n");
	if (uMyLength != uGapLength)
		Quit("Lengths differ");

	}

static SCORE ScoreSeqPair(const MSA &msa1, unsigned uSeqIndex1,
  const MSA &msa2, unsigned uSeqIndex2, SCORE *ptrLetters, SCORE *ptrGaps)
	{
	g_ptrMSA1.get() = &msa1;
	g_ptrMSA2.get() = &msa2;
	g_uSeqIndex1.get() = uSeqIndex1;
	g_uSeqIndex2.get() = uSeqIndex2;

	const unsigned uColCount = msa1.GetColCount();
	const unsigned uColCount2 = msa2.GetColCount();
	if (uColCount != uColCount2)
		Quit("ScoreSeqPair, different lengths");

#if	TRACE
	Log("ScoreSeqPair\n");
	Log("%16.16s  ", msa1.GetSeqName(uSeqIndex1));
	for (unsigned i = 0; i < uColCount; ++i)
		Log("%c", msa1.GetChar(uSeqIndex1, i));
	Log("\n");
	Log("%16.16s  ", msa2.GetSeqName(uSeqIndex2));
	for (unsigned i = 0; i < uColCount; ++i)
		Log("%c", msa1.GetChar(uSeqIndex2, i));
	Log("\n");
//.........这里部分代码省略.........

static void LogGap(unsigned uStart, unsigned uEnd, unsigned uGapLength,
  bool bNTerm, bool bCTerm)
	{
	Log("%16.16s  ", "");
	for (unsigned i = 0; i < uStart; ++i)
		Log(" ");
	unsigned uMyLength = 0;
	for (unsigned i = uStart; i <= uEnd; ++i)
		{
		bool bGap1 = g_ptrMSA1.get()->IsGap(g_uSeqIndex1.get(), i);
		bool bGap2 = g_ptrMSA2.get()->IsGap(g_uSeqIndex2.get(), i);
		if (!bGap1 && !bGap2)
			Quit("Error -- neither gapping");
		if (bGap1 && bGap2)
			Log(".");
		else
			{
			++uMyLength;
			Log("-");
			}
		}
	SCORE s = GapPenalty(uGapLength, bNTerm || bCTerm);
	Log(" L=%d N%d C%d s=%.3g", uGapLength, bNTerm, bCTerm, s);
	Log("\n");
	if (uMyLength != uGapLength)
		Quit("Lengths differ");

	}

static inline unsigned TriangleSubscript(unsigned uIndex1, unsigned uIndex2)
	{
#if	DEBUG
	if (uIndex1 >= g_uLeafCount.get() || uIndex2 >= g_uLeafCount.get())
		Quit("TriangleSubscript(%u,%u) %u", uIndex1, uIndex2, g_uLeafCount.get());
#endif
	unsigned v;
	if (uIndex1 >= uIndex2)
		v = uIndex2 + (uIndex1*(uIndex1 - 1))/2;
	else
		v = uIndex1 + (uIndex2*(uIndex2 - 1))/2;
	assert(v < (g_uLeafCount.get()*(g_uLeafCount.get() - 1))/2);
	return v;
	}

void Adapter::enableIndications(
    CMPIIndicationMI* mi,
    const CMPIContext* context)
{
    TRACE;

    _context_tls.set((void*)context);
    Adapter* adapter = (Adapter*)mi->hdl;
    Auto_RMutex auto_lock(adapter->_lock);

    // Ignore request if indications already enabled.

    if (adapter->_indications_enabled)
        return;

    adapter->_indications_enabled = true;

    // Invoke the provider:

    Enable_Indications_Status status = adapter->enable_indications(
        _indication_proc, adapter);

    switch (status)
    {
        case ENABLE_INDICATIONS_OK:
            break;

        case ENABLE_INDICATIONS_FAILED:
            break;
    }
}

void Adapter::disableIndications(
    CMPIIndicationMI* mi,
    const CMPIContext* context)
{
    TRACE;

    _context_tls.set((void*)context);
    Adapter* adapter = (Adapter*)mi->hdl;
    Auto_RMutex auto_lock(adapter->_lock);

    // Ignore if indications are not enabled.

    if (!adapter->_indications_enabled)
        return;

    // Invoke the provider:

    Disable_Indications_Status status = adapter->disable_indications();

    switch (status)
    {
        case DISABLE_INDICATIONS_OK:
            break;

        case DISABLE_INDICATIONS_FAILED:
            break;
    }

    adapter->_indications_enabled = false;
}

CMPIStatus Adapter::associators(
    CMPIAssociationMI* mi,
    const CMPIContext* context,
    const CMPIResult* result,
    const CMPIObjectPath* cmpi_op,
    const char* assoc_class_,
    const char* result_class_,
    const char* role_,
    const char* result_role_,
    const char** properties)
{
    TRACE;

    const char* assoc_class = assoc_class_ ? assoc_class_ : "";
    const char* result_class = result_class_ ? result_class_ : "";
    const char* role = role_ ? role_ : "";
    const char* result_role = result_role_ ? result_role_ : "";

    _context_tls.set((void*)context);
    Adapter* adapter = (Adapter*)mi->hdl;
    Auto_RMutex auto_lock(adapter->_lock);

    CIMPLE_ASSERT(strcasecmp(assoc_class, adapter->_mc->name) == 0);

    // Lookup meta class for cmpi_op (not the same as the provider class).

    const Meta_Class* mc = adapter->_find_meta_class(class_name(cmpi_op));

    if (!mc)
        CMReturn(CMPI_RC_ERR_INVALID_CLASS);

    // Convert to CIMPLE reference:

    Instance* cimple_ref = 0;
    CMPIrc rc = make_cimple_reference(mc, cmpi_op, cimple_ref);
    Destroyer<Instance> cimple_ref_d(cimple_ref);

    if (rc != CMPI_RC_OK)
        CMReturn(rc);

    // Invoke the provider:

    associators::Data data = { adapter->broker,
        context, result, name_space(cmpi_op), properties, CMPI_RC_OK };

    Enum_Associator_Names_Status status = adapter->enum_associator_names(
        cimple_ref,
        result_class,
        role,
        result_role,
        associators::_proc,
        &data);

    CMReturn(CMPI_RC_OK);
}

CMPIStatus Adapter::enumInstanceNames(
    CMPIInstanceMI* mi,
    const CMPIContext* context,
    const CMPIResult* result,
    const CMPIObjectPath* cmpi_op)
{
    TRACE;

    _context_tls.set((void*)context);
    Adapter* adapter = (Adapter*)mi->hdl;
    Auto_RMutex auto_lock(adapter->_lock);

    // Convert to CIMPLE reference:

    const Meta_Class* mc = adapter->_mc;
    Instance* cimple_ref = 0;

    CMPIrc rc = make_cimple_reference(mc, cmpi_op, cimple_ref);

    if (rc != CMPI_RC_OK)
        CMReturn(rc);

    Destroyer<Instance> cimple_ref_d(cimple_ref);

    // Nullify non-key properties (this is a reference).

    nullify_non_keys(cimple_ref);

    // Invoke provider:

    const char* ns = name_space(cmpi_op);

    enum_instance_names::Data data =
        { adapter->broker, result, ns, CMPI_RC_OK };

    Enum_Instances_Status status =
        adapter->enum_instances(cimple_ref, enum_instance_names::_proc, &data);

    switch (status)
    {
        case ENUM_INSTANCES_OK:
            CMReturnDone(result);
            CMReturn(CMPI_RC_OK);

        case ENUM_INSTANCES_FAILED:
            CMReturn(CMPI_RC_ERR_FAILED);
    }

    // Unreachable!
    CMReturn(CMPI_RC_OK);
}

CMPIStatus Adapter::enumInstances(
    CMPIInstanceMI* mi,
    const CMPIContext* context,
    const CMPIResult* result,
    const CMPIObjectPath* cmpi_op,
    const char** properties)
{
    TRACE;

    _context_tls.set((void*)context);
    Adapter* adapter = (Adapter*)mi->hdl;
    Auto_RMutex auto_lock(adapter->_lock);

    // Convert to CIMPLE reference:

    const Meta_Class* mc = adapter->_mc;
    Instance* cimple_ref = 0;

    CMPIrc rc = make_cimple_reference(mc, cmpi_op, cimple_ref);

    Destroyer<Instance> cimple_ref_d(cimple_ref);

    if (rc != CMPI_RC_OK)
        CMReturn(rc);

    // Filter properties:

    if (properties)
        filter_properties(cimple_ref, properties);

    // Invoke provider:

    enum_instances::Data data =
        { adapter->broker, result, cmpi_op, properties, CMPI_RC_OK };

    Enum_Instances_Status status =
        adapter->enum_instances(cimple_ref, enum_instances::_proc, &data);

    switch (status)
    {
        case ENUM_INSTANCES_OK:
            break;

        case ENUM_INSTANCES_FAILED:
            CMReturn(CMPI_RC_ERR_FAILED);
    }

    CMReturnDone(result);
    CMReturn(CMPI_RC_OK);
}

CMPIStatus Adapter::modifyInstance(
    CMPIInstanceMI* mi,
    const CMPIContext* context,
    const CMPIResult* result,
    const CMPIObjectPath* cmpi_op,
    const CMPIInstance* cmpi_inst,
    const char** properties)
{
    TRACE;

    _context_tls.set((void*)context);
    Adapter* adapter = (Adapter*)mi->hdl;
    Auto_RMutex auto_lock(adapter->_lock);

    // Create CIMPLE instance:

    const Meta_Class* mc = adapter->_mc;

    Instance* cimple_inst = 0;
    CMPIrc rc = make_cimple_instance(mc, cmpi_inst, cimple_inst);

    if (rc != CMPI_RC_OK)
        CMReturn(rc);

    Destroyer<Instance> cmpi_inst_d(cimple_inst);

    // Invoke the provider:

    Modify_Instance_Status status =
        adapter->modify_instance(cimple_inst);

    switch (status)
    {
        case MODIFY_INSTANCE_OK:
            CMReturnObjectPath(result, cmpi_op);
            CMReturnDone(result);
            CMReturn(CMPI_RC_OK);

        case MODIFY_INSTANCE_NOT_FOUND:
            CMReturn(CMPI_RC_ERR_NOT_FOUND);

        case MODIFY_INSTANCE_UNSUPPORTED:
            CMReturn(CMPI_RC_ERR_NOT_SUPPORTED);
    }

    CMReturn(CMPI_RC_OK);
}

void* Adapter::_timer_thread_proc(void* arg)
{
    TRACE;

    Adapter* adapter = (Adapter*)arg;

    CBAttachThread(adapter->broker, adapter->_timer_context);
    _context_tls.set((void*)adapter->_timer_context);

    // ATTN: there is currently no logic to stop this thread.

    while (!adapter->_stop_timer_thread)
        adapter->_sched->dispatch();

    CBDetachThread(adapter->broker, adapter->_timer_context);

    return 0;
}