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NCBI C++ ToolKit: CSraInputSource Class Reference
Search Toolkit Book for CSraInputSource
Class for reading sequences from SRA respository or SRA file. More...
#include <algo/blast/blast_sra_input/blast_sra_input.hpp>
CSraInputSource (const vector< string > &accessions, bool check_for_paires=true, bool cache_enabled=false) Constructor. More...
virtual ~CSraInputSource () virtual int GetNextSequence (CBioseq_set &bioseq_set) Get one sequence (or a pair for NGS reads) More...
virtual bool End (void) Signal whether there are any unread sequence left. More...
virtual SSeqLoc GetNextSSeqLoc (CScope &scope) Retrieve a single sequence (in an SSeqLoc container) More...
virtual CRef< CBlastSearchQuery > GetNextSequence (CScope &scope) Retrieve a single sequence (in a CBlastSearchQuery container) 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 virtual ~CBlastInputSourceOMF ()
Class for reading sequences from SRA respository or SRA file.
Definition at line 45 of file blast_sra_input.hpp.
◆ CSraInputSource() [1/2] ◆ ~CSraInputSource() virtual CSraInputSource::~CSraInputSource ( ) inlinevirtual
Definition at line 60 of file blast_sra_input.hpp.
◆ CSraInputSource() [2/2] ◆ End() bool CSraInputSource::End ( void ) virtual ◆ GetNextSequence() [1/2] ◆ GetNextSequence() [2/2] ◆ GetNextSSeqLoc() ◆ operator=() ◆ x_GetNextSeq_loc()
Read the next sequence, add it to scope and return Seq-loc object.
Definition at line 207 of file blast_sra_input.cpp.
References CScope::AddTopLevelSeqEntry(), CRef< C, Locker >::Empty(), eNa_strand_both, CBioseq::GetFirstId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), m_Accessions, m_BasesAdded, m_It, m_ItAcc, CSeq_loc::SetInt(), x_NextAccession(), and x_ReadOneSeq().
Referenced by GetNextSequence(), and GetNextSSeqLoc().
◆ x_NextAccession() void CSraInputSource::x_NextAccession ( void ) private ◆ x_ReadOneSeq() [1/2] ◆ x_ReadOneSeq() [2/2]
Read one sequence pointed by the iterator.
Definition at line 110 of file blast_sra_input.cpp.
References _ASSERT, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eRepr_raw, CTempString::length(), m_BasesAdded, m_It, CRef< C, Locker >::NotEmpty(), CBioseq_Base::SetAnnot(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), and CSeq_entry_Base::SetSeq().
Referenced by GetNextSequence(), x_GetNextSeq_loc(), x_ReadOneSeq(), and x_ReadPairs().
◆ x_ReadPairs() void CSraInputSource::x_ReadPairs ( CBioseq_set & bioseq_set ) private
Read one batch of sequences and mark pairs.
Definition at line 148 of file blast_sra_input.cpp.
References CUser_object::AddField(), eFirstSegment, eLastSegment, first(), m_Accessions, m_It, m_ItAcc, CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), x_NextAccession(), and x_ReadOneSeq().
Referenced by GetNextSequence().
◆ m_Accessions vector<string> CSraInputSource::m_Accessions private ◆ m_BasesAdded TSeqPos CSraInputSource::m_BasesAdded private ◆ m_IsPaired bool CSraInputSource::m_IsPaired private ◆ m_It ◆ m_ItAcc vector<string>::iterator CSraInputSource::m_ItAcc private ◆ m_SraDb unique_ptr<CCSraDb> CSraInputSource::m_SraDb private
The documentation for this class was generated from the following files:
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