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CSeqMaskerOstatBin Class Reference

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Compute and save counts information in simple binary format. More...

#include <algo/winmask/seq_masker_ostat_bin.hpp>

+ Inheritance diagram for CSeqMaskerOstatBin:
+ Collaboration diagram for CSeqMaskerOstatBin:

Public Member Functions

 CSeqMaskerOstatBin (const string &name, string const &metadata)
 Object constructor. More...
 
 CSeqMaskerOstatBin (CNcbiOstream &os, string const &metadata)
 Object constructor. More...
 
virtual ~CSeqMaskerOstatBin ()
 Object destructor. More...
 
virtual CSeqMaskerVersion constGetStatFmtVersion () const
 Get actual counts format version. 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...
 
CObjectoperator= (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 constSTAT_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 doSetUnitCount (Uint4 unit, Uint4 count)
 Write count information for the unit to the binary output. More...
 
virtual void doFinalize ()
 Write data to output file. 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 doSetUnitSize (Uint4 us)
 
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

void write_word (Uint4 word)
 

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< Uint8TCounter
 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
CNcbiOstreamout_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< Uint4pvalues
 
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

Compute and save counts information in simple binary format.

Definition at line 46 of file seq_masker_ostat_bin.hpp.

Constructor & Destructor Documentation

◆ CSeqMaskerOstatBin() [1/2]

CSeqMaskerOstatBin::CSeqMaskerOstatBin ( const string name,
string const metadata 
)
explicit

Object constructor.

Parameters
namethe name of the output file stream

Definition at line 55 of file seq_masker_ostat_bin.cpp.

◆ CSeqMaskerOstatBin() [2/2]

CSeqMaskerOstatBin::CSeqMaskerOstatBin ( CNcbiOstream os,
string const metadata 
)
explicit

Object constructor.

Parameters
osthe output stream

Definition at line 63 of file seq_masker_ostat_bin.cpp.

References write_word().

◆ ~CSeqMaskerOstatBin()

CSeqMaskerOstatBin::~CSeqMaskerOstatBin ( )
virtual

Object destructor.

Definition at line 69 of file seq_masker_ostat_bin.cpp.

Member Function Documentation

◆ doFinalize()

void CSeqMaskerOstatBin::doFinalize ( )
protectedvirtual

◆ doSetUnitCount()

void CSeqMaskerOstatBin::doSetUnitCount ( Uint4  unit,
Uint4  count 
)
protectedvirtual

Write count information for the unit to the binary output.

Parameters
unitthe unit
countthe number of times the unit and its reverse complement appears in the genome

Implements CSeqMaskerOstat.

Definition at line 80 of file seq_masker_ostat_bin.cpp.

References CSeqMaskerOstat::counts.

◆ GetStatFmtVersion()

virtual CSeqMaskerVersion const& CSeqMaskerOstatBin::GetStatFmtVersion ( ) const
inlinevirtual

Get actual counts format version.

Implements CSeqMaskerOstat.

Definition at line 72 of file seq_masker_ostat_bin.hpp.

References FormatVersion.

◆ write_word()

void CSeqMaskerOstatBin::write_word ( Uint4  word)
private

Definition at line 74 of file seq_masker_ostat_bin.cpp.

References CSeqMaskerOstat::out_stream.

Referenced by CSeqMaskerOstatBin(), and doFinalize().

Member Data Documentation

◆ FormatVersion

CSeqMaskerVersion CSeqMaskerOstatBin::FormatVersion
static

Format version.

Definition at line 51 of file seq_masker_ostat_bin.hpp.

Referenced by CWinMaskApplication::CWinMaskApplication(), and GetStatFmtVersion().


The documentation for this class was generated from the following files:
Modified on Thu Feb 22 17:12:00 2024 by modify_doxy.py rev. 669887