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CTrans_table Class Reference

Search Toolkit Book for CTrans_table

#include <objects/seqfeat/Genetic_code_table.hpp>

+ Inheritance diagram for CTrans_table:
+ Collaboration diagram for CTrans_table:

Public Member Functions

 CTrans_table (const CGenetic_code &)
 
 ~CTrans_table (void)
 
char GetCodonResidue (int state) const
 
char GetStartResidue (int state) const
 
char GetStopResidue (int state) const
 
bool IsOrfStart (int state) const
 
bool IsAmbigStart (int state) const
 
bool IsAnyStart (int state) const
 
bool IsOrfStop (int state) const
 
bool IsATGStart (int state) const
 
bool IsAltStart (int state) const
 
- 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 Member Functions

static int SetCodonState (unsigned char ch1, unsigned char ch2, unsigned char ch3)
 
static int NextCodonState (int state, unsigned char ch)
 
static int RevCompState (int state)
 
- 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)
 

Private Member Functions

void x_InitFsaTransl (const string *ncbieaa, const string *sncbieaa) const
 

Static Private Member Functions

static void x_InitFsaTable (void)
 

Private Attributes

char m_AminoAcid [4097]
 
char m_OrfStart [4097]
 
char m_OrfStop [4097]
 

Static Private Attributes

static int sm_NextState [4097]
 
static int sm_RvCmpState [4097]
 
static int sm_BaseToIdx [256]
 

Friends

class CGen_code_table_imp
 

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 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...
 

Detailed Description

Definition at line 93 of file Genetic_code_table.hpp.

Constructor & Destructor Documentation

◆ CTrans_table()

CTrans_table::CTrans_table ( const CGenetic_code gc)

◆ ~CTrans_table()

CTrans_table::~CTrans_table ( void  )

Definition at line 60 of file Genetic_code_table.cpp.

Member Function Documentation

◆ GetCodonResidue()

char CTrans_table::GetCodonResidue ( int  state) const
inline

◆ GetStartResidue()

char CTrans_table::GetStartResidue ( int  state) const
inline

◆ GetStopResidue()

char CTrans_table::GetStopResidue ( int  state) const
inline

Definition at line 240 of file Genetic_code_table.hpp.

References m_OrfStop.

Referenced by IsOrfStop(), and x_Translate().

◆ IsAltStart()

bool CTrans_table::IsAltStart ( int  state) const
inline

Definition at line 278 of file Genetic_code_table.hpp.

References IsOrfStart().

Referenced by x_Translate(), and CSFTranslationJob::x_Translate().

◆ IsAmbigStart()

bool CTrans_table::IsAmbigStart ( int  state) const
inline

Definition at line 253 of file Genetic_code_table.hpp.

References GetStartResidue().

◆ IsAnyStart()

bool CTrans_table::IsAnyStart ( int  state) const
inline

Definition at line 259 of file Genetic_code_table.hpp.

References GetStartResidue().

Referenced by CScore_StartStopCodon::Get().

◆ IsATGStart()

bool CTrans_table::IsATGStart ( int  state) const
inline

Definition at line 271 of file Genetic_code_table.hpp.

References IsOrfStart().

◆ IsOrfStart()

bool CTrans_table::IsOrfStart ( int  state) const
inline

◆ IsOrfStop()

bool CTrans_table::IsOrfStop ( int  state) const
inline

◆ NextCodonState()

int CTrans_table::NextCodonState ( int  state,
unsigned char  ch 
)
inlinestatic

◆ RevCompState()

int CTrans_table::RevCompState ( int  state)
inlinestatic

Definition at line 219 of file Genetic_code_table.hpp.

References sm_RvCmpState.

◆ SetCodonState()

int CTrans_table::SetCodonState ( unsigned char  ch1,
unsigned char  ch2,
unsigned char  ch3 
)
inlinestatic

◆ x_InitFsaTable()

void CTrans_table::x_InitFsaTable ( void  )
staticprivate

◆ x_InitFsaTransl()

void CTrans_table::x_InitFsaTransl ( const string ncbieaa,
const string sncbieaa 
) const
private

Definition at line 139 of file Genetic_code_table.cpp.

References eBase_A, eBase_C, eBase_G, eBase_gap, eBase_N, eBase_T, i, m_AminoAcid, m_OrfStart, m_OrfStop, and r().

Referenced by CTrans_table().

Friends And Related Function Documentation

◆ CGen_code_table_imp

friend class CGen_code_table_imp
friend

Definition at line 139 of file Genetic_code_table.hpp.

Member Data Documentation

◆ m_AminoAcid

char CTrans_table::m_AminoAcid[4097]
mutableprivate

Definition at line 131 of file Genetic_code_table.hpp.

Referenced by GetCodonResidue(), and x_InitFsaTransl().

◆ m_OrfStart

char CTrans_table::m_OrfStart[4097]
mutableprivate

Definition at line 132 of file Genetic_code_table.hpp.

Referenced by GetStartResidue(), and x_InitFsaTransl().

◆ m_OrfStop

char CTrans_table::m_OrfStop[4097]
mutableprivate

Definition at line 133 of file Genetic_code_table.hpp.

Referenced by GetStopResidue(), and x_InitFsaTransl().

◆ sm_BaseToIdx

int CTrans_table::sm_BaseToIdx
staticprivate

Definition at line 125 of file Genetic_code_table.hpp.

Referenced by NextCodonState(), SetCodonState(), and x_InitFsaTable().

◆ sm_NextState

int CTrans_table::sm_NextState
staticprivate

◆ sm_RvCmpState

int CTrans_table::sm_RvCmpState
staticprivate

Definition at line 124 of file Genetic_code_table.hpp.

Referenced by RevCompState(), and x_InitFsaTable().


The documentation for this class was generated from the following files:
Modified on Thu Nov 30 04:54:35 2023 by modify_doxy.py rev. 669887