NCBI C++ ToolKit
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Search Toolkit Book for CFastaBioseqSource
Public Member Functions | |
CFastaBioseqSource (CNcbiIstream &fasta_file, bool is_protein, bool parse_ids, bool long_ids) | |
~CFastaBioseqSource () | |
virtual CConstRef< CBioseq > | GetNext () |
Get a Bioseq object if there are any more to get. 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 Attributes | |
CRef< ILineReader > | m_LineReader |
CFastaReader * | m_FastaReader |
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< Uint8 > | TCounter |
Counter type is CAtomiCounter. More... | |
typedef Uint8 | TCount |
Alias for value type of counter. More... | |
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... | |
Definition at line 685 of file build_db.cpp.
CFastaBioseqSource::CFastaBioseqSource | ( | CNcbiIstream & | fasta_file, |
bool | is_protein, | ||
bool | parse_ids, | ||
bool | long_ids | ||
) |
Definition at line 701 of file build_db.cpp.
References ILineError::eProblem_ModifierFoundButNoneExpected, ILineError::eProblem_TooLong, ILineError::eProblem_TooManyAmbiguousResidues, CFastaReader::fAssumeNuc, CFastaReader::fAssumeProt, CFastaReader::fDisableNoResidues, CFastaReader::fForceType, flags, CFastaReader::fNoParseID, CFastaReader::fParseGaps, CFastaReader::fParseRawID, CFastaReader::fQuickIDCheck, CFastaReader::fRequireID, IRegistry::Get(), CNcbiApplicationAPI::GetConfig(), CFastaReader::IgnoreProblem(), CNcbiApplication::Instance(), m_FastaReader, m_LineReader, registry, CRef< C, Locker >::Reset(), CFastaReader::SetMaxIDLength(), NStr::StringToUInt(), and rapidjson::value.
CFastaBioseqSource::~CFastaBioseqSource | ( | ) |
Definition at line 750 of file build_db.cpp.
References m_FastaReader.
Get a Bioseq object if there are any more to get.
This method should return Bioseq objects one at a time until there are no more to get, then it should return NULL.
Implements IBioseqSource.
Definition at line 755 of file build_db.cpp.
References _ASSERT, ILineReader::AtEOF(), CConstRef< C, Locker >::Empty(), NStr::Find(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::IsSeq(), m_FastaReader, m_LineReader, msg(), NCBI_THROW, CRef< C, Locker >::NotEmpty(), NPOS, CFastaReader::ReadOneSeq(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), NStr::StartsWith(), and string.
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Definition at line 698 of file build_db.cpp.
Referenced by CFastaBioseqSource(), GetNext(), and ~CFastaBioseqSource().
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private |
Definition at line 697 of file build_db.cpp.
Referenced by CFastaBioseqSource(), and GetNext().