NCBI C++ ToolKit
Public Types | Public Member Functions | Private Types | Private Attributes | List of all members
CRepeatLibrary Class Reference

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Class acting as an interface to a RepeatMasker library. More...

#include <objtools/readers/rm_reader.hpp>

+ Inheritance diagram for CRepeatLibrary:
+ Collaboration diagram for CRepeatLibrary:

Public Types

typedef SRepeat TRepeat
 
- 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

 CRepeatLibrary (const ITaxonomyResolver &taxonomy)
 
bool Get (const string &name, TRepeat &dest) const
 Gets information about a given repeat, specified by name. More...
 
void Read (CNcbiIstream &stream)
 Reads a library from the RepeatMaskerLib.embl-style input. More...
 
bool TestSpecificityMatchesName (TRepeat::TTaxId taxid, const string &name) const
 Check if a given taxid's scientific name matches the original specificity string. More...
 
- 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 Types

typedef map< string, TRepeatTMap
 
typedef map< string, TRepeat::TTaxIdTSpecificity2Taxid
 

Private Attributes

CConstIRef< ITaxonomyResolverm_Taxonomy
 
TMap m_Map
 
TSpecificity2Taxid m_Specificity2TaxId
 
string m_Release
 

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...
 

Detailed Description

Class acting as an interface to a RepeatMasker library.

Definition at line 420 of file rm_reader.hpp.

Member Typedef Documentation

◆ TMap

Definition at line 444 of file rm_reader.hpp.

◆ TRepeat

Definition at line 423 of file rm_reader.hpp.

◆ TSpecificity2Taxid

Definition at line 445 of file rm_reader.hpp.

Constructor & Destructor Documentation

◆ CRepeatLibrary()

CRepeatLibrary::CRepeatLibrary ( const ITaxonomyResolver taxonomy)
inline

Definition at line 425 of file rm_reader.hpp.

Member Function Documentation

◆ Get()

bool CRepeatLibrary::Get ( const string name,
TRepeat dest 
) const

Gets information about a given repeat, specified by name.

Definition at line 262 of file rm_reader.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and m_Map.

◆ Read()

void CRepeatLibrary::Read ( CNcbiIstream stream)

◆ TestSpecificityMatchesName()

bool CRepeatLibrary::TestSpecificityMatchesName ( TRepeat::TTaxId  taxid,
const string name 
) const

Check if a given taxid's scientific name matches the original specificity string.

Definition at line 376 of file rm_reader.cpp.

References m_Taxonomy.

Member Data Documentation

◆ m_Map

TMap CRepeatLibrary::m_Map
private

Definition at line 448 of file rm_reader.hpp.

Referenced by Get(), and Read().

◆ m_Release

string CRepeatLibrary::m_Release
private

Definition at line 450 of file rm_reader.hpp.

Referenced by Read().

◆ m_Specificity2TaxId

TSpecificity2Taxid CRepeatLibrary::m_Specificity2TaxId
private

Definition at line 449 of file rm_reader.hpp.

Referenced by Read().

◆ m_Taxonomy

CConstIRef<ITaxonomyResolver> CRepeatLibrary::m_Taxonomy
private

Definition at line 447 of file rm_reader.hpp.

Referenced by Read(), and TestSpecificityMatchesName().


The documentation for this class was generated from the following files:
Modified on Mon May 20 05:00:15 2024 by modify_doxy.py rev. 669887