Search Toolkit Book for CSeqMaskerOstatOptAscii

This class is responsible for saving optimized unit counts in text format. More...

#include <algo/winmask/seq_masker_ostat_opt_ascii.hpp>

Inheritance diagram for CSeqMaskerOstatOptAscii:

Collaboration diagram for CSeqMaskerOstatOptAscii:

Public Member Functions
	CSeqMaskerOstatOptAscii (const string &name, Uint2 sz, string const &metadata)
	Object constructor. More...

	CSeqMaskerOstatOptAscii (CNcbiOstream &os, Uint2 sz, string const &metadata)
	Object constructor. More...

virtual	~CSeqMaskerOstatOptAscii ()
	Object destructor. More...

virtual CSeqMaskerVersion const &	GetStatFmtVersion () const
	Get actual counts format version. More...

Public Member Functions inherited from CSeqMaskerOstatOpt
	CSeqMaskerOstatOpt (CNcbiOstream &os, Uint2 sz, bool alloc, string const &metadata)
	Object constructor. More...

virtual	~CSeqMaskerOstatOpt ()
	Object destructor. More...

Public Member Functions inherited from CSeqMaskerOstat
	CSeqMaskerOstat (CNcbiOstream &os, bool alloc, string const &metadata)
	Object constructor. More...

virtual	~CSeqMaskerOstat ()
	Trivial object destructor. More...

void	setUnitSize (Uint1 us)
	Set the unit size value. More...

void	setUnitCount (Uint4 unit, Uint4 count)
	Add count value for a particular unit. More...

void	setComment (const string &msg)
	Add a comment to the unit counts file. More...

void	setParam (const string &name, Uint4 value)
	Set a value of a WindowMasker parameter. More...

void	finalize ()
	Perform any final tasks required to generate unit counts in the particular format. More...

void	SetStatAlgoVersion (CSeqMaskerVersion const &v)
	Set the counts generation algorithm version explicitly (needed for convertions). More...

void	SetMaxCount (Uint4 mc)

void	SetCount (Uint4 count, double pct)

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Static Public Attributes
static CSeqMaskerVersion	FormatVersion
	Format version. More...

Static Public Attributes inherited from CSeqMaskerOstat
static char const *	STAT_ALGO_COMPONENT_NAME

static CSeqMaskerVersion	StatAlgoVersion
	Version of the statistics generation algorithm. More...

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions
virtual void	write_out (const params &p) const
	Write optimized data to the output stream. More...

Protected Member Functions inherited from CSeqMaskerOstatOpt
Uint1	UnitSize () const
	Get the unit size value in bases. More...

const vector< Uint4 > &	GetParams () const
	Get the values of masking parameters. More...

virtual void	doSetUnitSize (Uint4 us)
	Set the unit size value. More...

virtual void	doSetUnitCount (Uint4 unit, Uint4 count)
	Set count information for the given unit. More...

virtual void	doFinalize ()
	Generate a hash function and dump the optimized unit counts data to the output stream. More...

Protected Member Functions inherited from CSeqMaskerOstat
string	FormatParameters () const
	Format algorithm parameters into a string. More...

string	FormatMetaData () const
	Combine version data and metadata into a single string. More...

void	WriteBinMetaData (std::ostream &os) const
	Write metadata in binary format. More...

virtual void	doSetComment (const string &)

virtual void	doSetParam (const string &, Uint4)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Protected Attributes inherited from CSeqMaskerOstat
CNcbiOstream &	out_stream
	Refers to the C++ stream that should be used to write out the unit counts data. More...

bool	alloc
	flag indicating that the stream was allocated More...

string	metadata
	metadata string More...

Uint1	unit_size
	unit size More...

vector< Uint4 >	pvalues

vector< pair< Uint4, Uint4 > >	counts
	Unit counts. More...

CSeqMaskerVersion	fmt_gen_algo_ver
	version of the algorithm used to generate counts More...

Uint4	max_count = 0
	information about counts and corresponding pct cutoffs More...

std::vector< double >	count_map

Static Protected Attributes inherited from CSeqMaskerOstat
static const char *	PARAMS [] = { "t_low", "t_extend", "t_threshold", "t_high" }
	Algorithm parameter names. More...