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NCBI C++ ToolKit: CUpdateSeq_Input Class Reference

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Sets up the old and the update sequences, and generates the alignment between them. More...

#include <gui/packages/pkg_sequence_edit/update_seq_input.hpp>

CUpdateSeq_Input (void) CUpdateSeq_Input (const objects::CBioseq_Handle &old_bsh, const objects::CBioseq_Handle &upd_bsh) ~CUpdateSeq_Input () const objects::CBioseq_Handle & GetOldBioseq (void) const objects::CBioseq_Handle GetNCOldBioseq (void) const const objects::CBioseq_Handle & GetUpdateBioseq (void) const CConstRef< objects::CSeq_align > GetAlignment (void) const void SetAlignment (const objects::CSeq_align *align) bool SetOldBioseqAndScope (IWorkbench *workbench, const objects::CSeq_entry_Handle &tse) bool SetOldBioseqAndScope (const objects::CBioseq_Handle &bsh) bool SetUpdateBioseq (const objects::CBioseq_Handle &bsh) bool ReadUpdateSequenceFromClipboard (objects::ILineErrorListener *msg_listener) Reads single update sequence from the clipboard. It supports FASTA and text ASN formats. More...
bool ReadSingleUpdateSequence (objects::ILineErrorListener *msg_listener) Reads (ASN.1 or FASTA) single update sequence from a file. More...
bool ReadSingleAccession (void) Reads single update sequence identified by an accession. More...
bool HaveIdenticalResidues (void) const bool IsReadyForUpdate (void) const bool UpdateSeqHasFeatures (void) const bool OldSeqHasFeatures (void) const bool OldSeqHasProteinFeats () const void CalculateAlignmentForUnitTest (void) Calculates the alignment between the old and the update sequence, sets m_Align member. More...
unsigned int CountBioseqs () void ResetUpdateSequence () 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

Sets up the old and the update sequences, and generates the alignment between them.

Definition at line 51 of file update_seq_input.hpp.

◆ CUpdateSeq_Input() [1/2] ◆ CUpdateSeq_Input() [2/2] CUpdateSeq_Input::CUpdateSeq_Input ( const objects::CBioseq_Handle & old_bsh, const objects::CBioseq_Handle & upd_bsh ) ◆ ~CUpdateSeq_Input() CUpdateSeq_Input::~CUpdateSeq_Input ( ) ◆ CalculateAlignmentForUnitTest() void CUpdateSeq_Input::CalculateAlignmentForUnitTest ( void )

Calculates the alignment between the old and the update sequence, sets m_Align member.

To be used only in the unit tests

Definition at line 188 of file update_seq_input.cpp.

References _ASSERT, sequpd::CompareAlignments(), i, Info(), CConstRef< C, Locker >::IsNull(), LOG_POST, m_Align, m_OldSeq, m_UpdSeq, CConstRef< C, Locker >::Reset(), and sequpd::RunBlast2Seq().

Referenced by SetupForUpdate(), and CUpdateMultipleSeq_Input::x_CreateUpdateSeqInputForUnitTest().

◆ CountBioseqs() unsigned int CUpdateSeq_Input::CountBioseqs ( ) ◆ GetAlignment() CConstRef<objects::CSeq_align> CUpdateSeq_Input::GetAlignment ( void ) const inline ◆ GetNCOldBioseq() objects::CBioseq_Handle CUpdateSeq_Input::GetNCOldBioseq ( void ) const inline ◆ GetOldBioseq() const objects::CBioseq_Handle& CUpdateSeq_Input::GetOldBioseq ( void ) const inline ◆ GetUpdateBioseq() const objects::CBioseq_Handle& CUpdateSeq_Input::GetUpdateBioseq ( void ) const inline ◆ HaveIdenticalResidues() bool CUpdateSeq_Input::HaveIdenticalResidues ( void ) const ◆ IsReadyForUpdate() bool CUpdateSeq_Input::IsReadyForUpdate ( void ) const ◆ OldSeqHasFeatures() bool CUpdateSeq_Input::OldSeqHasFeatures ( void ) const ◆ OldSeqHasProteinFeats() bool CUpdateSeq_Input::OldSeqHasProteinFeats ( ) const ◆ ReadSingleAccession() bool CUpdateSeq_Input::ReadSingleAccession ( void ) ◆ ReadSingleUpdateSequence() bool CUpdateSeq_Input::ReadSingleUpdateSequence ( objects::ILineErrorListener * msg_listener ) ◆ ReadUpdateSequenceFromClipboard() bool CUpdateSeq_Input::ReadUpdateSequenceFromClipboard ( objects::ILineErrorListener * msg_listener ) ◆ ResetUpdateSequence() void CUpdateSeq_Input::ResetUpdateSequence ( ) ◆ s_Align2IdenticalSeq() CRef< CSeq_annot > CUpdateSeq_Input::s_Align2IdenticalSeq ( const objects::CBioseq_Handle & subject, const objects::CBioseq_Handle & query ) static

Definition at line 92 of file update_seq_input.cpp.

References CSeq_id::Assign(), CSeq_align_Base::eType_partial, sequpd::HaveIdenticalResidues(), query, CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), CDense_seg_Base::SetDim(), CSeq_align_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CAnnotdesc_Base::SetName(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CSeq_align_Base::SetType(), and subject.

Referenced by BOOST_AUTO_TEST_CASE(), CUpdateMultiSeq_Dlg::x_CreateAlignmentForIdenticalUpdates(), and CUpdateMultiSeq_Dlg::x_GenerateAlignments().

◆ s_ConvertDeltaToRawBioseq() void CUpdateSeq_Input::s_ConvertDeltaToRawBioseq ( objects::CBioseq & bseq ) static ◆ s_ConvertDeltaToRawEntry() void CUpdateSeq_Input::s_ConvertDeltaToRawEntry ( objects::CSeq_entry & entry ) static

Converts delta literals to raw sequence, applies only to NA sequences.

Definition at line 498 of file update_seq_input.cpp.

References CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CBioseq::IsNa(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::IsSetSeq_set(), NON_CONST_ITERATE, s_ConvertDeltaToRawBioseq(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by x_ReadUpdateSeq_ASN().

◆ s_FixCollidingIDs_Entry() void CUpdateSeq_Input::s_FixCollidingIDs_Entry ( objects::CSeq_entry & entry, const objects::CBioseq::TId & seq_ids ) static

When the old and the update sequences have the same ID, the ID of the update sequence is modified.

Definition at line 531 of file update_seq_input.cpp.

References sequpd::FixCollidingIDs_Bioseq(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CBioseq::IsNa(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::IsSetSeq_set(), NON_CONST_ITERATE, CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by BOOST_AUTO_TEST_CASE(), and x_FixCollidingIDs_Entry().

◆ s_IsDeltaWithFarPointers() bool CUpdateSeq_Input::s_IsDeltaWithFarPointers ( const objects::CBioseq & bseq ) static

Definition at line 477 of file update_seq_input.cpp.

References CSeq_inst_Base::eRepr_delta, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetRepr(), CSeq_ext_Base::IsDelta(), CSeq_inst_Base::IsSetExt(), CBioseq_Base::IsSetInst(), and CSeq_inst_Base::IsSetRepr().

Referenced by CSequenceUpdater::CSequenceUpdater(), CSequenceUpdater::IsOldSequenceOK(), CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), and CUpdateSeqPanel::x_SetUpdateTypes().

◆ s_IsDeltaWithNoGaps() bool CUpdateSeq_Input::s_IsDeltaWithNoGaps ( const objects::CBioseq & bseq ) static

Definition at line 452 of file update_seq_input.cpp.

References CSeq_inst_Base::eRepr_delta, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CSeq_literal_Base::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_ext_Base::IsDelta(), CSeq_inst_Base::IsSetExt(), CBioseq_Base::IsSetInst(), CSeq_inst_Base::IsSetRepr(), ok, and s_IsGoodLiteral().

Referenced by CSequenceUpdater::IsOldSequenceOK(), s_ConvertDeltaToRawBioseq(), CSequenceUpdater::s_UpdateSeqInst(), CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), x_ReadAccession(), CSequenceUpdater::x_ReplaceSequence(), and CUpdateSeqPanel::x_SetUpdateTypes().

◆ s_IsGoodLiteral() bool CUpdateSeq_Input::s_IsGoodLiteral ( const objects::CSeq_literal & lit ) static ◆ SetAlignment() void CUpdateSeq_Input::SetAlignment ( const objects::CSeq_align * align ) inline ◆ SetOldBioseqAndScope() [1/2] bool CUpdateSeq_Input::SetOldBioseqAndScope ( const objects::CBioseq_Handle & bsh ) ◆ SetOldBioseqAndScope() [2/2] ◆ SetUpdateBioseq() bool CUpdateSeq_Input::SetUpdateBioseq ( const objects::CBioseq_Handle & bsh ) ◆ UpdateSeqHasFeatures() bool CUpdateSeq_Input::UpdateSeqHasFeatures ( void ) const ◆ x_AddNewEntryToScope() void CUpdateSeq_Input::x_AddNewEntryToScope ( CRef< objects::CSeq_entry > entry ) private ◆ x_FixCollidingIDs_Bioseq() void CUpdateSeq_Input::x_FixCollidingIDs_Bioseq ( objects::CBioseq & bioseq ) private ◆ x_FixCollidingIDs_Entry() void CUpdateSeq_Input::x_FixCollidingIDs_Entry ( objects::CSeq_entry & entry ) private ◆ x_ReadAccession()

Definition at line 601 of file update_seq_input.cpp.

References CSerialObject::Assign(), CSeq_id_Base::e_not_set, CBioseq_Handle::eCoding_Iupac, CBioseq_Base::GetId(), CMappedFeat::GetLocationId(), CSeqVector::GetSeqData(), ITERATE, m_Scope, m_UpdSeq, msg(), NcbiMessageBox(), CSeqportUtil::Pack(), CSeq_inst_Base::ResetExt(), s_IsDeltaWithNoGaps(), CSeq_id::Set(), CBioseq_EditHandle::SetInst(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), and CSeq_id_Handle::Which().

Referenced by ReadSingleAccession().

◆ x_ReadFromStream() bool CUpdateSeq_Input::x_ReadFromStream ( CNcbiIstream & istr, objects::ILineErrorListener * msg_listener ) private

Definition at line 285 of file update_seq_input.cpp.

References CFormatGuess::CFormatHints::AddPreferredFormat(), CFormatGuess::CFormatHints::DisableAllNonpreferred(), CFormatGuess::eFasta, CSeqUpdateException::eReading, CFormatGuess::eTextASN, CFormatGuess::eUnknown, format, CException::GetErrCode(), CFormatGuess::GetFormatHints(), CException::GetMsg(), CFormatGuess::GuessFormat(), NCBI_THROW, x_ReadUpdateSeq_ASN(), and x_ReadUpdateSeq_Fasta().

Referenced by ReadSingleUpdateSequence(), and ReadUpdateSequenceFromClipboard().

◆ x_ReadUpdateSeq_ASN()

Definition at line 327 of file update_seq_input.cpp.

References eNoOwnership, Error(), eSerial_AsnText, CException::GetMsg(), CObjectTypeInfo::GetName(), CObjectInfo::GetObjectPtr(), kNASeqCouldNotRead, LOG_POST, m_Scope, m_UpdSeq, NCBI_THROW, CObjectIStream::Open(), Ref(), s_ConvertDeltaToRawBioseq(), s_ConvertDeltaToRawEntry(), CTypeConverter< T >::SafeCast(), SeqEntryFromSeqSubmit(), x_AddNewEntryToScope(), and x_FixCollidingIDs_Bioseq().

Referenced by x_ReadFromStream().

◆ x_ReadUpdateSeq_Fasta() bool CUpdateSeq_Input::x_ReadUpdateSeq_Fasta ( CNcbiIstream & istr, objects::ILineErrorListener * msg_listener ) private

Definition at line 374 of file update_seq_input.cpp.

References ILineErrorListener::Count(), ILineError::ErrorMessage(), CFastaReader::fAssumeNuc, CFastaReader::fDLOptional, CFastaReader::fHyphensIgnoreAndWarn, flags, CFastaReader::fNoSplit, ILineErrorListener::GetError(), kMax_Int, kNASeqCouldNotRead, m_UpdSeq, NCBI_THROW, CFastaReader::ReadSet(), and x_AddNewEntryToScope().

Referenced by x_ReadFromStream().

◆ m_Align CConstRef<objects::CSeq_align> CUpdateSeq_Input::m_Align private ◆ m_OldSeq objects::CBioseq_Handle CUpdateSeq_Input::m_OldSeq private ◆ m_Scope CRef<objects::CScope> CUpdateSeq_Input::m_Scope private ◆ m_UpdSeq objects::CBioseq_Handle CUpdateSeq_Input::m_UpdSeq private

Definition at line 121 of file update_seq_input.hpp.

Referenced by CalculateAlignmentForUnitTest(), CountBioseqs(), GetUpdateBioseq(), HaveIdenticalResidues(), IsReadyForUpdate(), ReadSingleAccession(), ReadSingleUpdateSequence(), ReadUpdateSequenceFromClipboard(), ResetUpdateSequence(), SetUpdateBioseq(), UpdateSeqHasFeatures(), x_AddNewEntryToScope(), x_ReadAccession(), x_ReadUpdateSeq_ASN(), x_ReadUpdateSeq_Fasta(), and ~CUpdateSeq_Input().

The documentation for this class was generated from the following files:

include/gui/packages/pkg_sequence_edit/update_seq_input.hpp
src/gui/packages/pkg_sequence_edit/update_seq_input.cpp

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