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CTabularFormatter_ExonIntrons Class Reference

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formatter for dumping exons More...

#include <algo/align/util/tabular_fmt.hpp>

+ Inheritance diagram for CTabularFormatter_ExonIntrons:
+ Collaboration diagram for CTabularFormatter_ExonIntrons:

Public Types

enum  EIntervalType { e_Exons , e_Introns }
 
enum  EInfoType { e_Range , e_Length }
 
- 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...
 

Public Member Functions

 CTabularFormatter_ExonIntrons (unsigned sequence, EIntervalType interval, EInfoType info)
 
void PrintHelpText (CNcbiOstream &ostr) const
 
void PrintHeader (CNcbiOstream &ostr) const
 
void Print (CNcbiOstream &ostr, const objects::CSeq_align &align)
 
- Public Member Functions inherited from CTabularFormatter::IFormatter
virtual ~IFormatter ()
 
void SetScoreLookup (objects::CScoreLookup *scores)
 
virtual void SetGencoll (CConstRef< objects::CGC_Assembly >)
 
- 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
 

Private Attributes

unsigned m_Sequence
 
EIntervalType m_Interval
 
EInfoType m_Info
 

Additional Inherited Members

- 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 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 inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CTabularFormatter::IFormatter
objects::CScoreLookup * m_Scores
 

Detailed Description

formatter for dumping exons

Definition at line 531 of file tabular_fmt.hpp.

Member Enumeration Documentation

◆ EInfoType

Enumerator
e_Range 
e_Length 

Definition at line 535 of file tabular_fmt.hpp.

◆ EIntervalType

Enumerator
e_Exons 
e_Introns 

Definition at line 534 of file tabular_fmt.hpp.

Constructor & Destructor Documentation

◆ CTabularFormatter_ExonIntrons()

CTabularFormatter_ExonIntrons::CTabularFormatter_ExonIntrons ( unsigned  sequence,
EIntervalType  interval,
EInfoType  info 
)
inline

Definition at line 536 of file tabular_fmt.hpp.

Member Function Documentation

◆ Print()

void CTabularFormatter_ExonIntrons::Print ( CNcbiOstream ostr,
const objects::CSeq_align &  align 
)
virtual

◆ PrintHeader()

void CTabularFormatter_ExonIntrons::PrintHeader ( CNcbiOstream ostr) const
virtual

Implements CTabularFormatter::IFormatter.

Definition at line 1352 of file tabular_fmt.cpp.

References e_Exons, e_Introns, e_Length, e_Range, m_Info, m_Interval, and m_Sequence.

Referenced by Print().

◆ PrintHelpText()

void CTabularFormatter_ExonIntrons::PrintHelpText ( CNcbiOstream ostr) const
virtual

Implements CTabularFormatter::IFormatter.

Definition at line 1322 of file tabular_fmt.cpp.

References e_Exons, e_Introns, e_Length, e_Range, m_Info, m_Interval, and m_Sequence.

Member Data Documentation

◆ m_Info

EInfoType CTabularFormatter_ExonIntrons::m_Info
private

Definition at line 551 of file tabular_fmt.hpp.

Referenced by Print(), PrintHeader(), and PrintHelpText().

◆ m_Interval

EIntervalType CTabularFormatter_ExonIntrons::m_Interval
private

Definition at line 550 of file tabular_fmt.hpp.

Referenced by Print(), PrintHeader(), and PrintHelpText().

◆ m_Sequence

unsigned CTabularFormatter_ExonIntrons::m_Sequence
private

Definition at line 549 of file tabular_fmt.hpp.

Referenced by Print(), PrintHeader(), and PrintHelpText().


The documentation for this class was generated from the following files:
Modified on Wed Feb 21 09:58:05 2024 by modify_doxy.py rev. 669887