Search Toolkit Book for CSeqMaskerOstatOpt

Class responsible for collecting unit counts statistics and representing it in optimized hash-based format. More...

#include <algo/winmask/seq_masker_ostat_opt.hpp>

Inheritance diagram for CSeqMaskerOstatOpt:

Collaboration diagram for CSeqMaskerOstatOpt:

Classes
class	Exception
	Exceptions that CSeqMaskerOstatOpt might throw. More...

struct	params
	Parameters of the optimized data structure. More...

Public Member Functions
	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...

virtual CSeqMaskerVersion const &	GetStatFmtVersion () const =0
	Get actual counts format version. 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

Protected Member Functions
virtual void	write_out (const params &p) const =0
	Dump the unit counts data to the output stream according to the requested format. More...

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...

Private Member Functions
Uint1	findBestRoff (Uint1 k, Uint1 &max_coll, Uint4 &M, Uint4 *ht)

void	createCacheBitArray (Uint4 **cba)

Private Attributes
Uint2	size_requested

Uint1	unit_bit_size

vector< Uint4 >	units

vector< Uint2 >	counts

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)

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 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...

Detailed Description

Class responsible for collecting unit counts statistics and representing it in optimized hash-based format.

Definition at line 48 of file seq_masker_ostat_opt.hpp.

Constructor & Destructor Documentation

◆ CSeqMaskerOstatOpt()

CSeqMaskerOstatOpt::CSeqMaskerOstatOpt	(	CNcbiOstream &	os,
		Uint2	sz,
		bool	alloc,
		string const &	metadata
	)

explicit

Object constructor.

Parameters

os	output stream object, forwarded to CSeqMaskerOstream base
sz	requested size of the unit counts file in megabytes
alloc	flag to indicate that the stream was allocated

Definition at line 61 of file seq_masker_ostat_opt.cpp.

◆ ~CSeqMaskerOstatOpt()

virtual CSeqMaskerOstatOpt::~CSeqMaskerOstatOpt ( )

inlinevirtual

Object destructor.

Definition at line 86 of file seq_masker_ostat_opt.hpp.

Member Function Documentation

◆ createCacheBitArray()

void CSeqMaskerOstatOpt::createCacheBitArray ( Uint4 ** cba )

private

Definition at line 120 of file seq_masker_ostat_opt.cpp.

References _TRACE, counts, ERR_POST, i, CSeqMaskerUtil::reverse_complement(), ncbi::grid::netcache::search::fields::size, unit_bit_size, units, and Warning().

Referenced by doFinalize().

◆ doFinalize()

void CSeqMaskerOstatOpt::doFinalize ( )

protectedvirtual

Generate a hash function and dump the optimized unit counts data to the output stream.

Reimplemented from CSeqMaskerOstat.

Definition at line 212 of file seq_masker_ostat_opt.cpp.

References _TRACE, counts, createCacheBitArray(), findBestRoff(), AutoPtr< X, Del >::get(), CSeqMaskerUtil::hash_code(), i, LOG_POST, M, MB, NCBI_THROW, AutoPtr< X, Del >::reset(), size_requested, unit_bit_size, units, and write_out().

◆ doSetUnitCount()

void CSeqMaskerOstatOpt::doSetUnitCount	(	Uint4	unit,
		Uint4	count
	)

protectedvirtual

Set count information for the given unit.

Parameters

unit	the unit
count	the number of times the unit and its reverse complement appears in the genome

Implements CSeqMaskerOstat.

Definition at line 82 of file seq_masker_ostat_opt.cpp.

References count, counts, GROW_CHUNK, max(), and units.

◆ doSetUnitSize()

void CSeqMaskerOstatOpt::doSetUnitSize ( Uint4 us )

protectedvirtual

Set the unit size value.

Parameters

us	the unit size

Reimplemented from CSeqMaskerOstat.

Definition at line 75 of file seq_masker_ostat_opt.cpp.

References CSeqMaskerOstat::doSetUnitSize(), and unit_bit_size.

◆ findBestRoff()

Uint1 CSeqMaskerOstatOpt::findBestRoff	(	Uint1	k,
		Uint1 &	max_coll,
		Uint4 &	M,
		Uint4 *	ht
	)

private

Definition at line 163 of file seq_masker_ostat_opt.cpp.

References CSeqMaskerUtil::hash_code(), i, l(), M, t, unit_bit_size, and units.

Referenced by doFinalize().

◆ GetParams()

const vector< Uint4 > & CSeqMaskerOstatOpt::GetParams ( ) const

protected

Get the values of masking parameters.

Masking parameters is a vector of 4 integers representing the values of T_low, T_extend, T_threshold, and T_high.

Returns: vector of masking parameters

Definition at line 71 of file seq_masker_ostat_opt.cpp.

References CSeqMaskerOstat::pvalues.

Referenced by CSeqMaskerOstatOptBin::write_out(), and CSeqMaskerOstatOptAscii::write_out().

◆ UnitSize()

Uint1 CSeqMaskerOstatOpt::UnitSize ( ) const

protected

Get the unit size value in bases.

Returns: unit size

Definition at line 67 of file seq_masker_ostat_opt.cpp.

References unit_bit_size.

Referenced by CSeqMaskerOstatOptBin::write_out(), and CSeqMaskerOstatOptAscii::write_out().

◆ write_out()

virtual void CSeqMaskerOstatOpt::write_out ( const params & p ) const

protectedpure virtual

Dump the unit counts data to the output stream according to the requested format.

Derived classes should override this function to format the data.

Parameters

p	data structure parameters

Implemented in CSeqMaskerOstatOptAscii, and CSeqMaskerOstatOptBin.

Referenced by doFinalize().

Member Data Documentation

◆ counts

vector< Uint2 > CSeqMaskerOstatOpt::counts

private

Definition at line 177 of file seq_masker_ostat_opt.hpp.

Referenced by createCacheBitArray(), doFinalize(), and doSetUnitCount().

◆ size_requested

Uint2 CSeqMaskerOstatOpt::size_requested

private

Definition at line 173 of file seq_masker_ostat_opt.hpp.

Referenced by doFinalize().

◆ unit_bit_size

Uint1 CSeqMaskerOstatOpt::unit_bit_size

private

Definition at line 174 of file seq_masker_ostat_opt.hpp.

Referenced by createCacheBitArray(), doFinalize(), doSetUnitSize(), findBestRoff(), and UnitSize().

◆ units

vector< Uint4 > CSeqMaskerOstatOpt::units

private

Definition at line 176 of file seq_masker_ostat_opt.hpp.

Referenced by createCacheBitArray(), doFinalize(), doSetUnitCount(), and findBestRoff().

The documentation for this class was generated from the following files:

include/algo/winmask/seq_masker_ostat_opt.hpp
src/algo/winmask/seq_masker_ostat_opt.cpp

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CSeqMaskerOstatOpt()

◆ ~CSeqMaskerOstatOpt()

Member Function Documentation

◆ createCacheBitArray()

◆ doFinalize()

◆ doSetUnitCount()

◆ doSetUnitSize()

◆ findBestRoff()

◆ GetParams()

◆ UnitSize()

◆ write_out()

Member Data Documentation

◆ counts

◆ size_requested

◆ unit_bit_size

◆ units