Search Toolkit Book for CSraRun
#include <sra/readers/sra/sraread.hpp>
Inheritance diagram for CSraRun:
Collaboration diagram for CSraRun:
Public Member Functions | |
| CSraRun (void) | |
| CSraRun (CSraMgr &mgr, const string &acc) | |
| void | Init (CSraMgr &mgr, const string &acc) |
| const string & | GetAccession (void) const |
| CSeq_inst::TMol | GetSequenceType (spotid_t spot_id, uint8_t read_id) const |
| TSeqPos | GetSequenceLength (spotid_t spot_id, uint8_t read_id) const |
| CRef< CSeq_entry > | GetSpotEntry (spotid_t spot_id) const |
| Public Member Functions inherited from CSraRef< const SRATable > | |
| CSraRef (void) | |
| CSraRef (const TSelf &ref) | |
| CSraRef (TSelf &&ref) | |
| Copy constructor from an existing CRef object,. More... | |
| TSelf & | operator= (const TSelf &ref) |
| TSelf & | operator= (TSelf &&ref) |
| ~CSraRef (void) | |
| void | Release (void) |
| TObject * | GetPointer (void) const |
| operator TObject * (void) const | |
| TObject * | operator-> (void) const |
| TObject & | operator* (void) const |
Protected Member Functions | |
| void | x_DoInit (CSraMgr &mgr, const string &acc) |
| Protected Member Functions inherited from CSraRef< const SRATable > | |
| CSraRef (TPointer ptr) | |
| TObject ** | x_InitPtr (void) |
Private Attributes | |
| string | m_Acc |
| bool | m_Trim |
| CSraColumn | m_Name |
| CSraColumn | m_Read |
| CSraColumn | m_Qual |
| CSraColumn | m_SDesc |
| CSraColumn | m_RDesc |
| CSraColumn | m_TrimStart |
Additional Inherited Members | |
| Public Types inherited from CSraRef< const SRATable > | |
| typedef const SRATable | TObject |
| typedef TObject * | TPointer |
| Protected Types inherited from CSraRef< const SRATable > | |
| typedef CSraRef< const SRATable > | TSelf |
| typedef CSraRefTraits< const SRATable > | TTraits |
| Static Protected Member Functions inherited from CSraRef< const SRATable > | |
| static TObject * | s_AddRef (const TSelf &ref) |
Detailed Description
Definition at line 155 of file sraread.hpp.
Constructor & Destructor Documentation
◆ CSraRun() [1/2]
|
inline |
Definition at line 159 of file sraread.hpp.
◆ CSraRun() [2/2]
Definition at line 162 of file sraread.hpp.
References Init().
Member Function Documentation
◆ GetAccession()
Definition at line 169 of file sraread.hpp.
References m_Acc.
Referenced by CSRADataLoader_Impl::GetSequenceLength(), CSRADataLoader_Impl::GetSequenceType(), GetSpotEntry(), CSraMgr::GetSpotInfo(), and CSRADataLoader_Impl::LoadSRAEntry().
◆ GetSequenceLength()
Definition at line 613 of file sraread.cpp.
References kInvalidSeqPos, len, m_RDesc, m_SDesc, m_Trim, m_TrimStart, max(), min(), r(), and CSraValueFor< V >::Value().
Referenced by CSRADataLoader_Impl::GetSequenceLength().
◆ GetSequenceType()
| CSeq_inst::TMol CSraRun::GetSequenceType | ( | spotid_t | spot_id, |
| uint8_t | read_id | ||
| ) | const |
Definition at line 602 of file sraread.cpp.
References CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, and m_SDesc.
Referenced by CSRADataLoader_Impl::GetSequenceType().
◆ GetSpotEntry()
| CRef< CSeq_entry > CSraRun::GetSpotEntry | ( | spotid_t | spot_id | ) | const |
Definition at line 497 of file sraread.cpp.
References CSeq_entry::CSeq_entry(), CSraStringValue::data(), CBioseq_set_Base::eClass_other, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eRepr_raw, GetAccession(), CBioseq_set_Base::GetSeq_set(), i, kMax_Int, kMin_Int, len, m_Name, m_Qual, m_RDesc, m_Read, m_SDesc, m_Trim, m_TrimStart, max(), min(), NStr::NumericToString(), r(), CRef< C, Locker >::Reset(), CBioseq_Base::SetAnnot(), CByte_graph_Base::SetAxis(), CBioseq_set_Base::SetClass(), CSeq_annot_Base::SetData(), CBioseq_Base::SetDescr(), CSeq_graph_Base::SetGraph(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetLength(), CBioseq_set_Base::SetLevel(), CSeq_graph_Base::SetLoc(), CByte_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CSeq_inst_Base::SetMol(), CSeq_graph_Base::SetNumval(), CSeq_inst_Base::SetRepr(), CSeq_entry_Base::SetSeq(), CSeq_inst_Base::SetSeq_data(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CSeq_graph_Base::SetTitle(), CSeqdesc_Base::SetTitle(), CByte_graph_Base::SetValues(), NStr::UIntToString(), CSraStringValue::Value(), and CSraValueFor< V >::Value().
Referenced by CSraMgr::GetSpotEntry(), and CSRADataLoader_Impl::LoadSRAEntry().
◆ Init()
Definition at line 452 of file sraread.cpp.
References CSraMgr::GetTrim(), m_Acc, m_Trim, and x_DoInit().
Referenced by CSraRun(), CSRADataLoader_Impl::GetSequenceLength(), CSRADataLoader_Impl::GetSequenceType(), and CSRADataLoader_Impl::LoadSRAEntry().
◆ x_DoInit()
Definition at line 460 of file sraread.cpp.
References CHECK_VDB_TIMEOUT_FMT, CSraColumn::Init(), m_Name, m_Qual, m_RDesc, m_Read, m_SDesc, m_TrimStart, NCBI_THROW3, CSraColumn::TryInitRc(), and CSraRef< const SRATable >::x_InitPtr().
Referenced by Init().
Member Data Documentation
◆ m_Acc
|
private |
Definition at line 182 of file sraread.hpp.
Referenced by GetAccession(), and Init().
◆ m_Name
|
private |
Definition at line 184 of file sraread.hpp.
Referenced by GetSpotEntry(), and x_DoInit().
◆ m_Qual
|
private |
Definition at line 186 of file sraread.hpp.
Referenced by GetSpotEntry(), and x_DoInit().
◆ m_RDesc
|
private |
Definition at line 188 of file sraread.hpp.
Referenced by GetSequenceLength(), GetSpotEntry(), and x_DoInit().
◆ m_Read
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private |
Definition at line 185 of file sraread.hpp.
Referenced by GetSpotEntry(), and x_DoInit().
◆ m_SDesc
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private |
Definition at line 187 of file sraread.hpp.
Referenced by GetSequenceLength(), GetSequenceType(), GetSpotEntry(), and x_DoInit().
◆ m_Trim
|
private |
Definition at line 183 of file sraread.hpp.
Referenced by GetSequenceLength(), GetSpotEntry(), and Init().
◆ m_TrimStart
|
private |
Definition at line 189 of file sraread.hpp.
Referenced by GetSequenceLength(), GetSpotEntry(), and x_DoInit().
The documentation for this class was generated from the following files:
- include/sra/readers/sra/sraread.hpp
- src/sra/readers/sra/sraread.cpp
