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NCBI C++ ToolKit: CRepeatLibrary Class Reference
Search Toolkit Book for CRepeatLibrary
Class acting as an interface to a RepeatMasker library. More...
#include <objtools/readers/rm_reader.hpp>
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...
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...
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
Class acting as an interface to a RepeatMasker library.
Definition at line 420 of file rm_reader.hpp.
◆ TMap ◆ TRepeat ◆ TSpecificity2Taxid ◆ CRepeatLibrary() ◆ Get() ◆ Read()
Reads a library from the RepeatMaskerLib.embl-style input.
Definition at line 270 of file rm_reader.cpp.
References map_checker< Container >::clear(), Convert(), ERR_POST, map_checker< Container >::insert(), kInvalidSeqPos, m_Map, m_Release, SRepeat::m_RptClass, SRepeat::m_RptFamily, SRepeat::m_RptLength, SRepeat::m_RptName, SRepeat::m_RptRepbaseId, SRepeat::m_RptSpecificity, SRepeat::m_RptSpecificityName, m_Specificity2TaxId, m_Taxonomy, NStr::MatchesMask(), NcbiGetlineEOL(), NStr::StartsWith(), NStr::TruncateSpaces(), NStr::TruncateSpacesInPlace(), rapidjson::value, and Warning().
◆ TestSpecificityMatchesName() ◆ m_Map TMap CRepeatLibrary::m_Map private ◆ m_Release string CRepeatLibrary::m_Release private ◆ m_Specificity2TaxId ◆ m_Taxonomy
The documentation for this class was generated from the following files:
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