Search Toolkit Book for CRepeatLibrary
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< Uint8 > | TCounter |
| 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... | |
| 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... | |
| 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, TRepeat > | TMap |
| typedef map< string, TRepeat::TTaxId > | TSpecificity2Taxid |
Private Attributes | |
| CConstIRef< ITaxonomyResolver > | m_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
|
private |
Definition at line 444 of file rm_reader.hpp.
◆ TRepeat
| typedef SRepeat CRepeatLibrary::TRepeat |
Definition at line 423 of file rm_reader.hpp.
◆ TSpecificity2Taxid
|
private |
Definition at line 445 of file rm_reader.hpp.
Constructor & Destructor Documentation
◆ CRepeatLibrary()
|
inline |
Definition at line 425 of file rm_reader.hpp.
Member Function Documentation
◆ Get()
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 | ) |
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(), value, and Warning().
◆ 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
|
private |
Definition at line 448 of file rm_reader.hpp.
◆ m_Release
|
private |
Definition at line 450 of file rm_reader.hpp.
Referenced by Read().
◆ m_Specificity2TaxId
|
private |
Definition at line 449 of file rm_reader.hpp.
Referenced by Read().
◆ 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:
- include/objtools/readers/rm_reader.hpp
- src/objtools/readers/rm_reader.cpp
