Search Toolkit Book for CSeqMaskerOstat

Base class for computing and saving unit counts data. More...

#include <algo/winmask/seq_masker_ostat.hpp>

Inheritance diagram for CSeqMaskerOstat:

Collaboration diagram for CSeqMaskerOstat:

Classes
class	CSeqMaskerOstatException
	Exceptions that CSeqMaskerOstat can throw. More...

Public Member Functions
	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

Static Public Attributes
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
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...

Methods used to delegate functionality to derived classes
virtual void	doSetUnitSize (Uint4 us)

virtual void	doSetUnitCount (Uint4, Uint4)=0

virtual void	doSetComment (const string &)

virtual void	doSetParam (const string &, Uint4)

virtual void	doFinalize ()

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

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

Private Types
enum	{ start , ulen , udata , thres , final }

Private Member Functions
Provide reference semantics for the class
	CSeqMaskerOstat (const CSeqMaskerOstat &)

CSeqMaskerOstat &	operator= (const CSeqMaskerOstat &)

Private Attributes
enum CSeqMaskerOstat:: { ... }	state

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)

Detailed Description

Base class for computing and saving unit counts data.

Definition at line 50 of file seq_masker_ostat.hpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

private

Enumerator
start
ulen
udata
thres
final

Definition at line 226 of file seq_masker_ostat.hpp.

Constructor & Destructor Documentation

◆ CSeqMaskerOstat() [1/2]

CSeqMaskerOstat::CSeqMaskerOstat	(	CNcbiOstream &	os,
		bool	alloc,
		string const &	metadata
	)

explicit

Object constructor.

Parameters

os	C++ stream that should be used to save the unit counts data

Definition at line 52 of file seq_masker_ostat_opt.cpp.

◆ ~CSeqMaskerOstat()

virtual CSeqMaskerOstat::~CSeqMaskerOstat ( )

inlinevirtual

Trivial object destructor.

Definition at line 90 of file seq_masker_ostat.hpp.

References alloc, and out_stream.

◆ CSeqMaskerOstat() [2/2]

CSeqMaskerOstat::CSeqMaskerOstat ( const CSeqMaskerOstat & )

private

Member Function Documentation

◆ doFinalize()

virtual void CSeqMaskerOstat::doFinalize ( )

inlineprotectedvirtual

Reimplemented in CSeqMaskerOstatOpt, CSeqMaskerOstatBin, and CSeqMaskerOstatAscii.

Definition at line 173 of file seq_masker_ostat.hpp.

Referenced by finalize().

◆ doSetComment()

virtual void CSeqMaskerOstat::doSetComment ( const string & )

inlineprotectedvirtual

Reimplemented in CSeqMaskerOstatAscii.

Definition at line 170 of file seq_masker_ostat.hpp.

Referenced by setComment().

◆ doSetParam()

void CSeqMaskerOstat::doSetParam	(	const string &	name,
		Uint4	value
	)

protectedvirtual

Definition at line 103 of file seq_masker_ostat_opt.cpp.

References Error(), LOG_POST, PARAMS, and value.

Referenced by setParam().

◆ doSetUnitCount()

virtual void CSeqMaskerOstat::doSetUnitCount	(	Uint4	,
		Uint4
	)

protectedpure virtual

Implemented in CSeqMaskerOstatOpt, CSeqMaskerOstatBin, and CSeqMaskerOstatAscii.

Referenced by setUnitCount().

◆ doSetUnitSize()

virtual void CSeqMaskerOstat::doSetUnitSize ( Uint4 us )

inlineprotectedvirtual

Reimplemented in CSeqMaskerOstatOpt.

Definition at line 168 of file seq_masker_ostat.hpp.

References unit_size.

Referenced by CSeqMaskerOstatOpt::doSetUnitSize(), and setUnitSize().

◆ finalize()

void CSeqMaskerOstat::finalize ( )

Perform any final tasks required to generate unit counts in the particular format.

Definition at line 192 of file seq_masker_ostat.cpp.

References doFinalize(), NCBI_THROW, state, thres, and udata.

Referenced by CWinMaskCountsConverter::operator()(), and CWinMaskCountsGenerator::operator()().

◆ FormatMetaData()

string CSeqMaskerOstat::FormatMetaData ( ) const

protected

Combine version data and metadata into a single string.

Definition at line 128 of file seq_masker_ostat.cpp.

References count_map, fmt_gen_algo_ver, FormatParameters(), GetStatFmtVersion(), i, max_count, metadata, and CSeqMaskerVersion::Print().

Referenced by CSeqMaskerOstatAscii::doFinalize(), and CSeqMaskerOstatOptAscii::write_out().

◆ FormatParameters()

string CSeqMaskerOstat::FormatParameters ( ) const

protected

Format algorithm parameters into a string.

Definition at line 69 of file seq_masker_ostat.cpp.

References unit_size.

Referenced by FormatMetaData(), and WriteBinMetaData().

◆ GetStatFmtVersion()

virtual CSeqMaskerVersion const& CSeqMaskerOstat::GetStatFmtVersion ( ) const

pure virtual

Get actual counts format version.

Implemented in CSeqMaskerOstatOptBin, CSeqMaskerOstatOptAscii, CSeqMaskerOstatBin, and CSeqMaskerOstatAscii.

Referenced by FormatMetaData(), and WriteBinMetaData().

◆ operator=()

CSeqMaskerOstat& CSeqMaskerOstat::operator= ( const CSeqMaskerOstat & )

private

◆ setComment()

void CSeqMaskerOstat::setComment ( const string & msg )

inline

Add a comment to the unit counts file.

It is possible that this method is NOP for some unit counts formats.

Parameters

msg	comment message

Definition at line 121 of file seq_masker_ostat.hpp.

References doSetComment().

Referenced by CWinMaskCountsGenerator::operator()().

◆ SetCount()

void CSeqMaskerOstat::SetCount	(	Uint4	count,
		double	pct
	)

inline

Definition at line 155 of file seq_masker_ostat.hpp.

References assert, count_map, and max_count.

Referenced by CWinMaskCountsConverter::operator()(), and CWinMaskCountsGenerator::operator()().

◆ SetMaxCount()

void CSeqMaskerOstat::SetMaxCount ( Uint4 mc )

inline

Definition at line 149 of file seq_masker_ostat.hpp.

References count_map, and max_count.

Referenced by CWinMaskCountsConverter::operator()(), and CWinMaskCountsGenerator::operator()().

◆ setParam()

void CSeqMaskerOstat::setParam	(	const string &	name,
		Uint4	value
	)

Set a value of a WindowMasker parameter.

This method only can be called after all setUnitCount() calls.

Parameters

name	the name of the parameter
value	the value of the parameter

Definition at line 177 of file seq_masker_ostat.cpp.

References doSetParam(), NCBI_THROW, state, thres, udata, ulen, and value.

Referenced by CWinMaskCountsConverter::operator()(), and CWinMaskCountsGenerator::operator()().

◆ SetStatAlgoVersion()

void CSeqMaskerOstat::SetStatAlgoVersion ( CSeqMaskerVersion const & v )

inline

Set the counts generation algorithm version explicitly (needed for convertions).

Definition at line 142 of file seq_masker_ostat.hpp.

References fmt_gen_algo_ver.

Referenced by CWinMaskCountsConverter::operator()().

◆ setUnitCount()

void CSeqMaskerOstat::setUnitCount	(	Uint4	unit,
		Uint4	count
	)

Add count value for a particular unit.

This method can not be called before setUnitSize() and after the first call to setParam().

Parameters

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

Definition at line 162 of file seq_masker_ostat.cpp.

References doSetUnitCount(), NCBI_THROW, state, udata, and ulen.

Referenced by CWinMaskCountsConverter::operator()(), and CWinMaskCountsGenerator::process().

◆ setUnitSize()

void CSeqMaskerOstat::setUnitSize ( Uint1 us )

Set the unit size value.

This method must be called before any call to setUnitCount().

Parameters

us	new value of unit size

Definition at line 147 of file seq_masker_ostat.cpp.

References doSetUnitSize(), NCBI_THROW, start, state, and ulen.

Referenced by CWinMaskCountsConverter::operator()(), and CWinMaskCountsGenerator::operator()().

◆ WriteBinMetaData()

void CSeqMaskerOstat::WriteBinMetaData ( std::ostream & os ) const

protected

Write metadata in binary format.

Definition at line 78 of file seq_masker_ostat.cpp.

References count_map, fmt_gen_algo_ver, FormatParameters(), GetStatFmtVersion(), i, max_count, metadata, CSeqMaskerVersion::Print(), and string.

Referenced by CSeqMaskerOstatBin::doFinalize(), and CSeqMaskerOstatOptBin::write_out().

Member Data Documentation

◆ alloc

bool CSeqMaskerOstat::alloc

protected

flag indicating that the stream was allocated

Definition at line 192 of file seq_masker_ostat.hpp.

Referenced by ~CSeqMaskerOstat().

◆ count_map

std::vector< double > CSeqMaskerOstat::count_map

protected

Definition at line 213 of file seq_masker_ostat.hpp.

Referenced by FormatMetaData(), SetCount(), SetMaxCount(), and WriteBinMetaData().

◆ counts

vector< pair< Uint4, Uint4 > > CSeqMaskerOstat::counts

protected

Unit counts.

Definition at line 206 of file seq_masker_ostat.hpp.

Referenced by CSeqMaskerOstatAscii::doFinalize(), CSeqMaskerOstatBin::doFinalize(), CSeqMaskerOstatAscii::doSetUnitCount(), and CSeqMaskerOstatBin::doSetUnitCount().

◆ fmt_gen_algo_ver

CSeqMaskerVersion CSeqMaskerOstat::fmt_gen_algo_ver

protected

version of the algorithm used to generate counts

Definition at line 209 of file seq_masker_ostat.hpp.

Referenced by FormatMetaData(), SetStatAlgoVersion(), and WriteBinMetaData().

◆ max_count

Uint4 CSeqMaskerOstat::max_count = 0

protected

information about counts and corresponding pct cutoffs

Definition at line 212 of file seq_masker_ostat.hpp.

Referenced by FormatMetaData(), SetCount(), SetMaxCount(), and WriteBinMetaData().

◆ metadata

string CSeqMaskerOstat::metadata

protected

metadata string

Definition at line 195 of file seq_masker_ostat.hpp.

Referenced by FormatMetaData(), and WriteBinMetaData().

◆ out_stream

CNcbiOstream& CSeqMaskerOstat::out_stream

protected

Refers to the C++ stream that should be used to write out the unit counts data.

Definition at line 189 of file seq_masker_ostat.hpp.

Referenced by CSeqMaskerOstatAscii::doFinalize(), CSeqMaskerOstatBin::doFinalize(), CSeqMaskerOstatOptBin::write_out(), CSeqMaskerOstatOptAscii::write_out(), CSeqMaskerOstatBin::write_word(), CSeqMaskerOstatOptBin::write_word(), and ~CSeqMaskerOstat().

◆ PARAMS

const char * CSeqMaskerOstat::PARAMS = { "t_low", "t_extend", "t_threshold", "t_high" }

staticprotected

Algorithm parameter names.

Definition at line 164 of file seq_masker_ostat.hpp.

Referenced by doSetParam().

◆ pvalues

vector< Uint4 > CSeqMaskerOstat::pvalues

protected

Definition at line 203 of file seq_masker_ostat.hpp.

Referenced by CSeqMaskerOstatOpt::GetParams().

◆ STAT_ALGO_COMPONENT_NAME

char const * CSeqMaskerOstat::STAT_ALGO_COMPONENT_NAME

static

Initial value:

=

"windowmasker-statistics-algorithm-version"

Definition at line 54 of file seq_masker_ostat.hpp.

Referenced by CSeqMaskerIstatFactory::create(), and ExtractStatAlgoVersion().

◆ StatAlgoVersion

CSeqMaskerVersion CSeqMaskerOstat::StatAlgoVersion

static

Version of the statistics generation algorithm.

Definition at line 57 of file seq_masker_ostat.hpp.

Referenced by CWinMaskApplication::CWinMaskApplication().

◆

enum { ... } CSeqMaskerOstat::state

Referenced by finalize(), setParam(), setUnitCount(), and setUnitSize().

◆ unit_size

Uint1 CSeqMaskerOstat::unit_size

protected

unit size

Definition at line 198 of file seq_masker_ostat.hpp.

Referenced by CSeqMaskerOstatAscii::doFinalize(), CSeqMaskerOstatBin::doFinalize(), doSetUnitSize(), and FormatParameters().

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

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

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ anonymous enum

Constructor & Destructor Documentation

◆ CSeqMaskerOstat() [1/2]

◆ ~CSeqMaskerOstat()

◆ CSeqMaskerOstat() [2/2]

Member Function Documentation

◆ doFinalize()

◆ doSetComment()

◆ doSetParam()

◆ doSetUnitCount()

◆ doSetUnitSize()

◆ finalize()

◆ FormatMetaData()

◆ FormatParameters()

◆ GetStatFmtVersion()

◆ operator=()

◆ setComment()

◆ SetCount()

◆ SetMaxCount()

◆ setParam()

◆ SetStatAlgoVersion()

◆ setUnitCount()

◆ setUnitSize()

◆ WriteBinMetaData()

Member Data Documentation

◆ alloc

◆ count_map

◆ counts

◆ fmt_gen_algo_ver

◆ max_count

◆ metadata

◆ out_stream

◆ PARAMS

◆ pvalues

◆ STAT_ALGO_COMPONENT_NAME

◆ StatAlgoVersion

◆

◆ unit_size