CSequenceUpdater Class Reference

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Class responsible for executing the sequence update for one old-update sequence pair. More...

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

Collaboration diagram for CSequenceUpdater:

Public Member Functions
	CSequenceUpdater (const CUpdateSeq_Input &updseq_in, const SUpdateSeqParams &params)
	~CSequenceUpdater ()
void	SetUpdateSeqParams (const SUpdateSeqParams &params)
CRef< CCmdComposite >	Update (bool create_general_only)
	Main function responsible to update the old sequence with the update sequence. More...
bool	IsOldSequenceOK () const
bool	IsUpdateSequenceRaw () const
bool	IsAlignmentOK () const
bool	CheckParameters () const
const string &	GetCitSubMessage () const
void	ShowCitSubMessage (void) const
bool	IsReverseComplemented () const
string	GetRevCompReport () const
void	GetNotImportedFeatsReport (CNcbiOstream &out) const

Static Public Member Functions
static objects::CSeq_align::TDim	FindRowInAlignment (const objects::CBioseq_Handle &bsh, const objects::CSeq_align &align)
static CRef< objects::CSeq_inst >	s_ExtendOneEndOfSequence (const objects::CBioseq_Handle &bsh, const string &extension, SUpdateSeqParams::ESequenceUpdateType update_type)
	Extends the 5' or 3' end of a NA sequence (no alignment is necessary). More...
static CRef< objects::CSeq_inst >	s_UpdateSeqInst (const objects::CBioseq_Handle &bsh, const string &upd_str)
static string	s_GetValidExtension (const string &extension)
static CRef< objects::CSeq_feat >	s_OffsetFeature (const objects::CSeq_feat &feat, const TSeqPos offset, const objects::CSeq_id *newId=NULL)
	Offsets the location of the feature. More...
static void	s_Shift_CDSCodeBreaks (CRef< objects::CSeq_feat > feat, const TSeqPos &offset, const objects::CSeq_id *targetId=NULL)
static void	s_Shift_tRNAAntiCodon (CRef< objects::CSeq_feat > feat, const TSeqPos &offset, const objects::CSeq_id *targetId=NULL)
static CRef< objects::CSeq_loc >	s_OffsetLocation (const objects::CSeq_loc &sourceLoc, const TSeqPos &offset, const objects::CSeq_id *targetId=NULL)

Private Types
typedef list< CRef< objects::CSeq_feat > >	TFeatList

Private Member Functions
void	NoChange (bool create_general_only)
void	Replace (bool create_general_only)
void	Patch (bool create_general_only)
void	ExtendOneEndOfSequence (bool create_general_only)
CRef< objects::CSeq_inst >	x_ReplaceSequence ()
CRef< objects::CSeq_inst >	x_PatchSequence ()
CRef< objects::CSeq_inst >	x_ExtendOneEnd ()
CRef< objects::CSeq_inst >	x_UpdateSeqInst (const string &upd_str)
void	x_MakeNewEntry (const objects::CSeq_inst &newInst)
	Creates the new seq-entry. It is not added to the scope, yet. More...
void	x_PrepareNewEntry (CRef< objects::CSeq_entry > entry, const objects::CSeq_inst &newInst)
objects::CSeq_entry_Handle	x_GetOldBseq_EntryHandle (void)
CIRef< IEditCommand >	x_SwapOldWithNewSeq ()
	Creates command that swaps the old sequence with the new one. More...
bool	x_ShouldRemoveFeature (const objects::CSeq_feat_Handle &fh)
bool	x_ShouldImportFeature (const objects::CSeq_feat_Handle &fh)
	Determines whether the feature from update sequence should be imported to the new one. More...
void	x_ChangeIDInFeature (objects::CSeq_feat_Handle fh, const objects::CSeq_align &align, objects::CSeq_align::TDim row)
	Replaces the location ID in the feature to match the alignment ID corresponding to the given row. More...
CRef< objects::CSeq_feat >	x_MappedFeature_ChangeId (const objects::CSeq_feat_Handle &orig_fh)
	Changes only the location ID of the feature. More...
CRef< objects::CSeq_feat >	x_MappedFeature_ThroughAlign (const objects::CSeq_feat_Handle &orig_fh, const objects::CSeq_align &align)
	Maps feature's location through the alignment. More...
void	x_ReplaceIdInOldFeatures ()
void	x_MapOldAndImportedFeatsThroughNewAlign ()
CConstRef< objects::CSeq_align >	x_GetNewAlign_Replace (const objects::CBioseq_Handle &bsh)
vector< CConstRef< objects::CSeq_align > >	x_FormNewAlignment (const objects::CBioseq_Handle &subject)
	Generates alignment between subject_bsh and the new sequence (query) More...
void	x_HandleDuplicateFeatures ()
	Decides which duplicate features will end up on the new sequence. More...
CRef< objects::CSeq_feat >	x_FuseFeatures (const objects::CSeq_feat &feat1, const objects::CSeq_feat &feat2)
	Merges duplicate features. More...
void	x_FuseProtFeatsForCDS (const objects::CSeq_feat &fusedFeat, const objects::CSeq_feat &feat_old)
	Merges protein sequence features for duplicate coding regions. More...
void	x_FixID_AttachFeatures (bool create_general_only)
void	x_AttachFeaturesToNewSeq (bool create_general_only)
	Removes newId in features and stores them in two seq-annots: one that will be attached to the sequence and another one that will be attached to the set. More...
void	x_FixIDInNewEntry (CRef< objects::CSeq_entry > entry)
void	x_RemoveNewIDInFeature (CRef< objects::CSeq_feat > feat)
void	x_UpdateProteinID (CRef< objects::CSeq_entry > protein, CRef< objects::CSeq_id > newId)
void	x_AdjustProteinFeature (CRef< objects::CSeq_entry > protein, CRef< objects::CSeq_id > newId=CRef< objects::CSeq_id >())
void	x_SetOldIDInFeatures ()
CRef< objects::CSeq_annot >	x_GetSeqAnnot_WithoutCDS (bool &has_cds)
void	x_AdjustOldCDSProduct (CRef< objects::CSeq_feat > cds, objects::CSeq_entry_EditHandle &eh)
void	x_ImportCDSProduct (CRef< objects::CSeq_feat > cds, objects::CSeq_entry_EditHandle &eh, objects::CBioseq_Handle &newBsh, bool create_general_only)
void	x_RetranslateOldCDSProduct (CRef< objects::CSeq_feat > cds, objects::CSeq_entry_EditHandle &eh, objects::CBioseq_Handle &newBsh, bool create_general_only)
void	x_RetranslateImportedCDSProduct (CRef< objects::CSeq_feat > cds, objects::CSeq_entry_EditHandle &eh, objects::CBioseq_Handle &newBsh, bool create_general_only)
void	x_RemoveDescriptorsFromImportedProducts (CRef< objects::CSeq_entry > protein)
	Removes RefGeneTracking user-object and create-date descriptors from imported cds products. More...
void	x_AddCitSubToUpdatedSequence ()
	Attaches a cit-sub to the New sequence. More...
void	x_PrintNewEntryIds ()
TSeqPos	x_GetNewSeqLength ()
	CSequenceUpdater (const CSequenceUpdater &)
CSequenceUpdater &	operator= (const CSequenceUpdater &)

Private Attributes
objects::CBioseq_Handle	m_OldBsh
const objects::CBioseq_Handle &	m_UpdBsh
CConstRef< objects::CSeq_align >	m_Align
SUpdateSeqParams	m_Params
CRef< objects::CSeq_entry >	m_NewEntry
	The new seq-entry. More...
CConstRef< objects::CSeq_id >	m_NewId
	Temporary seq-id of the new seq-entry. More...
TFeatList	m_MappedOldFeats
	List of features, originally belonging to the Old Sequence and update sequence, respectively. More...
TFeatList	m_ImportUpdFeats
string	m_CitSubMessage
bool	m_Reversed
vector< string >	m_NotImportedFeats
	List of features that were not imported as they were outside the alignment range. More...

Detailed Description

Class responsible for executing the sequence update for one old-update sequence pair.

Definition at line 56 of file update_seq.hpp.

Member Typedef Documentation

TFeatList

typedef list<CRef<objects::CSeq_feat> > CSequenceUpdater::TFeatList

private

Definition at line 208 of file update_seq.hpp.

Constructor & Destructor Documentation

CSequenceUpdater() [1/2]

CSequenceUpdater::CSequenceUpdater	(	const CUpdateSeq_Input &	updseq_in,
		const SUpdateSeqParams &	params
	)

Definition at line 488 of file update_seq.cpp.

References CheckParameters(), IsAlignmentOK(), IsOldSequenceOK(), CUpdateSeq_Input::IsReadyForUpdate(), IsUpdateSequenceRaw(), m_UpdBsh, NCBI_THROW, and CUpdateSeq_Input::s_IsDeltaWithFarPointers().

~CSequenceUpdater()

CSequenceUpdater::~CSequenceUpdater

(

)

Definition at line 520 of file update_seq.cpp.

CSequenceUpdater() [2/2]

CSequenceUpdater::CSequenceUpdater ( const CSequenceUpdater &  )

private

Member Function Documentation

CheckParameters()

bool CSequenceUpdater::CheckParameters

(

)

const

Definition at line 548 of file update_seq.cpp.

References SUpdateSeqParams::eSeqUpdateExtend3, SUpdateSeqParams::eSeqUpdateExtend5, SUpdateSeqParams::eSeqUpdatePatch, m_Align, SUpdateSeqParams::m_IgnoreAlignment, m_Params, and SUpdateSeqParams::m_SeqUpdateOption.

Referenced by CSequenceUpdater().

ExtendOneEndOfSequence()

void CSequenceUpdater::ExtendOneEndOfSequence ( bool  create_general_only )

private

Definition at line 722 of file update_seq.cpp.

References SUpdateSeqParams::eSeqUpdateExtend3, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_any, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_IgnoreAlignment, SUpdateSeqParams::m_ImportFeatures, m_ImportUpdFeats, m_MappedOldFeats, m_NewId, m_OldBsh, m_Params, SUpdateSeqParams::m_SeqUpdateOption, m_UpdBsh, s_OffsetFeature(), SAnnotSelector::SetLimitTSE(), x_ExtendOneEnd(), x_FixID_AttachFeatures(), x_HandleDuplicateFeatures(), x_MakeNewEntry(), x_MapOldAndImportedFeatsThroughNewAlign(), and x_ShouldRemoveFeature().

Referenced by Update().

FindRowInAlignment()

CSeq_align::TDim CSequenceUpdater::FindRowInAlignment ( const objects::CBioseq_Handle &  bsh, const objects::CSeq_align &  align  )

static

Definition at line 611 of file update_seq.cpp.

References CSeq_align::CheckNumRows(), CSeq_align::GetSeq_id(), CBioseq_Handle::IsSynonym(), and row.

Referenced by GetNotImportedFeatsReport(), Replace(), x_ExtendOneEnd(), x_GetNewAlign_Replace(), CUpdateSeqPanel::x_InitDrawingParams(), x_MapOldAndImportedFeatsThroughNewAlign(), x_PatchSequence(), CUpdateSeqPanel::x_SetUpdateTypes(), x_ShouldImportFeature(), and x_ShouldRemoveFeature().

GetCitSubMessage()

const string& CSequenceUpdater::GetCitSubMessage ( ) const

inline

Definition at line 94 of file update_seq.hpp.

References m_CitSubMessage.

Referenced by BOOST_AUTO_TEST_CASE(), and CSeqUpdateWorker::x_LaunchSingleUpdateSequence().

GetNotImportedFeatsReport()

void CSequenceUpdater::GetNotImportedFeatsReport

(

CNcbiOstream &

out

)

const

Definition at line 2123 of file update_seq.cpp.

References _ASSERT, CSeq_id::eContent, eGetId_Best, FindRowInAlignment(), GetId(), CSeq_loc::GetLabel(), CSeq_id::GetLabel(), CSeq_id_Handle::GetSeqId(), m_Align, m_NotImportedFeats, m_UpdBsh, and out().

Referenced by CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), and CUpdateMultiSeq_Dlg::x_UpdateSelected().

GetRevCompReport()

string CSequenceUpdater::GetRevCompReport

(

)

const

Definition at line 2108 of file update_seq.cpp.

References CSeq_id::BestRank(), FindBestChoice(), CSeq_id::GetLabel(), kEmptyStr, m_OldBsh, and m_Reversed.

Referenced by CSeqUpdateWorker::x_LaunchSingleUpdateSequence().

IsAlignmentOK()

bool CSequenceUpdater::IsAlignmentOK

(

)

const

Definition at line 543 of file update_seq.cpp.

References m_Align.

Referenced by CSequenceUpdater().

IsOldSequenceOK()

bool CSequenceUpdater::IsOldSequenceOK

(

)

const

Definition at line 529 of file update_seq.cpp.

References CSeq_inst_Base::eRepr_raw, m_OldBsh, CUpdateSeq_Input::s_IsDeltaWithFarPointers(), and CUpdateSeq_Input::s_IsDeltaWithNoGaps().

Referenced by BOOST_AUTO_TEST_CASE(), and CSequenceUpdater().

IsReverseComplemented()

bool CSequenceUpdater::IsReverseComplemented ( ) const

inline

Definition at line 97 of file update_seq.hpp.

References m_Reversed.

Referenced by CUpdateMultiSeq_Dlg::x_UpdateSelected().

IsUpdateSequenceRaw()

bool CSequenceUpdater::IsUpdateSequenceRaw

(

)

const

Definition at line 538 of file update_seq.cpp.

References CSeq_inst_Base::eRepr_raw, and m_UpdBsh.

Referenced by BOOST_AUTO_TEST_CASE(), and CSequenceUpdater().

NoChange()

void CSequenceUpdater::NoChange ( bool  create_general_only )

private

Definition at line 640 of file update_seq.cpp.

References CSerialObject::Assign(), m_Align, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_ImportFeatures, m_ImportUpdFeats, m_OldBsh, m_Params, m_UpdBsh, SAnnotSelector::SetLimitTSE(), x_FixID_AttachFeatures(), x_GetNewAlign_Replace(), x_HandleDuplicateFeatures(), x_MakeNewEntry(), x_MappedFeature_ThroughAlign(), x_ReplaceIdInOldFeatures(), and x_ShouldImportFeature().

Referenced by Update().

operator=()

CSequenceUpdater& CSequenceUpdater::operator= ( const CSequenceUpdater &  )

private

Patch()

void CSequenceUpdater::Patch ( bool  create_general_only )

private

Definition at line 711 of file update_seq.cpp.

References _ASSERT, m_Align, x_FixID_AttachFeatures(), x_MakeNewEntry(), x_MapOldAndImportedFeatsThroughNewAlign(), and x_PatchSequence().

Referenced by Update().

Replace()

void CSequenceUpdater::Replace ( bool  create_general_only )

private

Definition at line 669 of file update_seq.cpp.

References CSeqFeatData::eSubtype_any, FindRowInAlignment(), m_Align, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_ImportFeatures, m_ImportUpdFeats, m_MappedOldFeats, m_OldBsh, m_Params, m_UpdBsh, SAnnotSelector::SetLimitTSE(), x_ChangeIDInFeature(), x_FixID_AttachFeatures(), x_GetNewAlign_Replace(), x_HandleDuplicateFeatures(), x_MakeNewEntry(), x_MappedFeature_ChangeId(), x_MappedFeature_ThroughAlign(), x_ReplaceIdInOldFeatures(), x_ReplaceSequence(), and x_ShouldRemoveFeature().

Referenced by Update().

s_ExtendOneEndOfSequence()

CRef< CSeq_inst > CSequenceUpdater::s_ExtendOneEndOfSequence ( const objects::CBioseq_Handle &  bsh, const string &  extension, SUpdateSeqParams::ESequenceUpdateType  update_type  )

static

Extends the 5' or 3' end of a NA sequence (no alignment is necessary).

Only valid residues are kept and used for sequence extension

Definition at line 953 of file update_seq.cpp.

References CBioseq_Handle::eCoding_Iupac, eNa_strand_plus, SUpdateSeqParams::eSeqUpdateExtend3, SUpdateSeqParams::eSeqUpdateExtend5, CBioseq_Handle::GetBioseqLength(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CBioseq_Handle::IsAa(), s_GetValidExtension(), and s_UpdateSeqInst().

Referenced by BOOST_AUTO_TEST_CASE(), CEditSequenceEnds::GetCommand(), and x_ExtendOneEnd().

s_GetValidExtension()

string CSequenceUpdater::s_GetValidExtension ( const string &  extension )

static

Definition at line 934 of file update_seq.cpp.

References kEmptyStr, NPOS, and NStr::ToLower().

Referenced by BOOST_AUTO_TEST_CASE(), and s_ExtendOneEndOfSequence().

s_OffsetFeature()

CRef< CSeq_feat > CSequenceUpdater::s_OffsetFeature ( const objects::CSeq_feat &  feat, const TSeqPos  offset, const objects::CSeq_id *  newId = NULL  )

static

Offsets the location of the feature.

If newId is not Null, it also changes the feature location ID

Definition at line 1014 of file update_seq.cpp.

References CSerialObject::Assign(), CSeqFeatData::eSubtype_tRNA, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsCdregion(), offset, s_OffsetLocation(), s_Shift_CDSCodeBreaks(), s_Shift_tRNAAntiCodon(), and CSeq_feat_Base::SetLocation().

Referenced by BOOST_AUTO_TEST_CASE(), ExtendOneEndOfSequence(), and CEditSequenceEnds::GetCommand().

s_OffsetLocation()

CRef< CSeq_loc > CSequenceUpdater::s_OffsetLocation ( const objects::CSeq_loc &  sourceLoc, const TSeqPos &  offset, const objects::CSeq_id *  targetId = NULL  )

static

Definition at line 1057 of file update_seq.cpp.

References CSeq_loc::Assign(), CRange_Base::GetFrom(), CSeq_loc_CI::GetRange(), CRange_Base::GetTo(), CSeq_loc_I::MakeSeq_loc(), offset, CSeq_loc_I::SetFrom(), CSeq_loc_I::SetSeq_id(), and CSeq_loc_I::SetTo().

Referenced by s_OffsetFeature(), s_Shift_CDSCodeBreaks(), and s_Shift_tRNAAntiCodon().

s_Shift_CDSCodeBreaks()

void CSequenceUpdater::s_Shift_CDSCodeBreaks ( CRef< objects::CSeq_feat >  feat, const TSeqPos &  offset, const objects::CSeq_id *  targetId = NULL  )

static

Definition at line 1030 of file update_seq.cpp.

References CCdregion_Base::IsSetCode_break(), NON_CONST_ITERATE, offset, s_OffsetLocation(), CCdregion_Base::SetCode_break(), and CSeq_feat_Base::SetData().

Referenced by s_OffsetFeature().

s_Shift_tRNAAntiCodon()

void CSequenceUpdater::s_Shift_tRNAAntiCodon ( CRef< objects::CSeq_feat >  feat, const TSeqPos &  offset, const objects::CSeq_id *  targetId = NULL  )

static

Definition at line 1044 of file update_seq.cpp.

References CTrna_ext_Base::GetAnticodon(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::GetTRNA(), CTrna_ext_Base::IsSetAnticodon(), CRNA_ref_Base::IsSetExt(), CRNA_ref_Base::C_Ext::IsTRNA(), offset, s_OffsetLocation(), CTrna_ext_Base::SetAnticodon(), CSeq_feat_Base::SetData(), and CRNA_ref_Base::C_Ext::SetTRNA().

Referenced by s_OffsetFeature().

s_UpdateSeqInst()

CRef< CSeq_inst > CSequenceUpdater::s_UpdateSeqInst ( const objects::CBioseq_Handle &  bsh, const string &  upd_str  )

static

Definition at line 988 of file update_seq.cpp.

References CSerialObject::Assign(), CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CBioseq_Handle::GetCompleteBioseq(), CBioseq_Handle::GetInst(), CBioseq_Handle::GetInst_Repr(), CConstRef< C, Locker >::GetObject(), NStr::IsBlank(), CBioseq_Handle::IsNa(), CSeqportUtil::Pack(), CSeq_inst_Base::ResetExt(), CUpdateSeq_Input::s_IsDeltaWithNoGaps(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), and CSeq_inst_Base::SetSeq_data().

Referenced by s_ExtendOneEndOfSequence(), and x_UpdateSeqInst().

SetUpdateSeqParams()

void CSequenceUpdater::SetUpdateSeqParams

(

const SUpdateSeqParams &

params

)

Definition at line 524 of file update_seq.cpp.

References m_Params.

ShowCitSubMessage()

void CSequenceUpdater::ShowCitSubMessage

(

void

)

const

Definition at line 2101 of file update_seq.cpp.

References m_CitSubMessage, and NcbiInfoBox().

Update()

CRef< CCmdComposite > CSequenceUpdater::Update

(

bool

create_general_only

)

Main function responsible to update the old sequence with the update sequence.

Definition at line 564 of file update_seq.cpp.

References CCmdComposite::AddCommand(), ConstRef(), CSeq_id_Base::e_Local, SUpdateSeqParams::eSeqUpdateExtend3, SUpdateSeqParams::eSeqUpdateExtend5, SUpdateSeqParams::eSeqUpdateNoChange, SUpdateSeqParams::eSeqUpdatePatch, SUpdateSeqParams::eSeqUpdateReplace, ExtendOneEndOfSequence(), kNewLocalID, SUpdateSeqParams::m_AddCitSub, m_Align, m_NewId, m_Params, m_Reversed, SUpdateSeqParams::m_SeqUpdateOption, NoChange(), Patch(), Replace(), CConstRef< C, Locker >::Reset(), SameOrientation(), x_AddCitSubToUpdatedSequence(), and x_SwapOldWithNewSeq().

Referenced by BOOST_AUTO_TEST_CASE(), CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), and CUpdateMultiSeq_Dlg::x_UpdateSelected().

x_AddCitSubToUpdatedSequence()

void CSequenceUpdater::x_AddCitSubToUpdatedSequence ( )

private

Attaches a cit-sub to the New sequence.

Definition at line 2032 of file update_seq.cpp.

References CScope::AddDefaults(), CSeq_entry_EditHandle::AddSeqdesc(), CScope::AddTopLevelSeqEntry(), CBioseq_set_Base::eClass_nuc_prot, NStr::EqualNocase(), CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetEditHandle(), CObjectManager::GetInstance(), CSeq_entry_EditHandle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), m_CitSubMessage, m_NewEntry, m_OldBsh, CSeq_entry_EditHandle::RemoveSeqdesc(), CRef< C, Locker >::Reset(), CCitSubUpdater::s_GetCitSubForUpdatedSequence(), and CCitSubUpdater::sm_ChangeExistingCitSub.

Referenced by Update().

x_AdjustOldCDSProduct()

void CSequenceUpdater::x_AdjustOldCDSProduct ( CRef< objects::CSeq_feat >  cds, objects::CSeq_entry_EditHandle &  eh  )

private

Definition at line 1788 of file update_seq.cpp.

References CSerialObject::Assign(), CSeq_entry_EditHandle::AttachEntry(), CScope::GetBioseqHandle(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_feat_Base::IsSetProduct(), and m_OldBsh.

Referenced by x_AttachFeaturesToNewSeq().

x_AdjustProteinFeature()

void CSequenceUpdater::x_AdjustProteinFeature ( CRef< objects::CSeq_entry >  protein, CRef< objects::CSeq_id >  newId = CRef<objects::CSeq_id>()  )

private

Definition at line 1986 of file update_seq.cpp.

References EDIT_EACH_FEATURE_ON_ANNOT, EDIT_EACH_SEQANNOT_ON_BIOSEQ, CSeq_feat_Base::GetData(), CBioseq::GetLength(), CSeqFeatData_Base::GetProt(), CSeq_entry_Base::GetSeq(), CSeq_annot::IsFtable(), CBioseq::IsNa(), CSeqFeatData_Base::IsProt(), CSeq_entry_Base::IsSet(), CSeq_feat_Base::IsSetData(), CProt_ref_Base::IsSetProcessed(), CBioseq_Base::ResetId(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), and CSeq_entry_Base::SetSeq().

Referenced by x_RetranslateImportedCDSProduct(), and x_RetranslateOldCDSProduct().

x_AttachFeaturesToNewSeq()

void CSequenceUpdater::x_AttachFeaturesToNewSeq ( bool  create_general_only )

private

Removes newId in features and stores them in two seq-annots: one that will be attached to the sequence and another one that will be attached to the set.

Definition at line 1647 of file update_seq.cpp.

References _ASSERT, CScope::AddDefaults(), CSeq_entry_EditHandle::AddSeqdesc(), CScope::AddTopLevelSeqEntry(), CBioseq_EditHandle::AttachAnnot(), CSeq_entry_EditHandle::AttachAnnot(), CSeq_entry_EditHandle::ConvertSeqToSet(), CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetClass(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CObjectManager::GetInstance(), CSeq_entry_EditHandle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CSeqFeatData_Base::IsCdregion(), CRef< C, Locker >::IsNull(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), CSeq_feat_Base::IsSetData(), m_ImportUpdFeats, m_MappedOldFeats, m_NewEntry, m_OldBsh, m_Params, SUpdateSeqParams::m_UpdateProteins, NON_CONST_ITERATE, CSeq_annot_Base::SetData(), CBioseq_EditHandle::SetDescr(), CSeq_entry_EditHandle::SetSet(), x_AdjustOldCDSProduct(), x_GetSeqAnnot_WithoutCDS(), x_ImportCDSProduct(), x_RetranslateImportedCDSProduct(), x_RetranslateOldCDSProduct(), and x_SetOldIDInFeatures().

Referenced by x_FixID_AttachFeatures().

x_ChangeIDInFeature()

void CSequenceUpdater::x_ChangeIDInFeature ( objects::CSeq_feat_Handle  fh, const objects::CSeq_align &  align, objects::CSeq_align::TDim  row  )

private

Replaces the location ID in the feature to match the alignment ID corresponding to the given row.

Definition at line 1345 of file update_seq.cpp.

References copy(), CSeqFeatData::eSubtype_tRNA, CSeq_feat_Handle::GetLocationId(), CSeq_feat_Handle::GetSeq_feat(), CSeq_align::GetSeq_id(), CCdregion_Base::IsSetCode_break(), NON_CONST_ITERATE, CSeq_feat_EditHandle::Replace(), rna, row, CCdregion_Base::SetCode_break(), CSeq_id_Handle::Which(), and CSeq_id_Base::Which().

Referenced by Replace(), and x_MapOldAndImportedFeatsThroughNewAlign().

x_ExtendOneEnd()

CRef< CSeq_inst > CSequenceUpdater::x_ExtendOneEnd ( )

private

Definition at line 879 of file update_seq.cpp.

References _ASSERT, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus, SUpdateSeqParams::eSeqUpdateExtend3, SUpdateSeqParams::eSeqUpdateExtend5, FindRowInAlignment(), CSeqVector::GetSeqData(), m_Align, SUpdateSeqParams::m_IgnoreAlignment, m_OldBsh, m_Params, SUpdateSeqParams::m_SeqUpdateOption, m_UpdBsh, s_ExtendOneEndOfSequence(), and x_UpdateSeqInst().

Referenced by ExtendOneEndOfSequence().

x_FixID_AttachFeatures()

void CSequenceUpdater::x_FixID_AttachFeatures ( bool  create_general_only )

private

Definition at line 767 of file update_seq.cpp.

References m_NewEntry, x_AttachFeaturesToNewSeq(), and x_FixIDInNewEntry().

Referenced by ExtendOneEndOfSequence(), NoChange(), Patch(), and Replace().

x_FixIDInNewEntry()

void CSequenceUpdater::x_FixIDInNewEntry ( CRef< objects::CSeq_entry >  entry )

private

Definition at line 1963 of file update_seq.cpp.

References CSeq_id::Assign(), CSeq_entry_Base::IsSeq(), ITERATE, m_NewEntry, m_OldBsh, CBioseq_Base::ResetId(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by x_FixID_AttachFeatures().

x_FormNewAlignment()

vector< CConstRef< objects::CSeq_align > > CSequenceUpdater::x_FormNewAlignment ( const objects::CBioseq_Handle &  subject )

private

Generates alignment between subject_bsh and the new sequence (query)

Definition at line 1384 of file update_seq.cpp.

References _ASSERT, ERR_POST, CSeq_entry_Handle::GetBioseqHandle(), CSeq_entry_Handle::GetEditHandle(), CSeq_entry_Handle::GetTopLevelEntry(), m_NewEntry, m_NewId, m_OldBsh, NCBI_THROW, CSeq_entry_EditHandle::Remove(), sequpd::RunBlast2Seq(), subject, and CException::what().

Referenced by x_MapOldAndImportedFeatsThroughNewAlign().

x_FuseFeatures()

CRef< CSeq_feat > CSequenceUpdater::x_FuseFeatures ( const objects::CSeq_feat &  feat1, const objects::CSeq_feat &  feat2  )

private

Merges duplicate features.

Definition at line 1468 of file update_seq.cpp.

References AddValueToString(), CSerialObject::Assign(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Region, CSeqFeatData_Base::e_Rna, eExistingText_append_semi, NStr::EqualNocase(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CSeqFeatData_Base::GetGene(), CRNA_ref_Base::C_Ext::GetName(), CSeqFeatData_Base::GetRegion(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::IsName(), CRNA_ref_Base::IsSetExt(), rna, CSeq_feat_Base::SetData(), CRNA_ref_Base::SetExt(), rapidjson::value, CSeqFeatData_Base::Which(), and x_FuseProtFeatsForCDS().

Referenced by x_FuseProtFeatsForCDS(), and x_HandleDuplicateFeatures().

x_FuseProtFeatsForCDS()

void CSequenceUpdater::x_FuseProtFeatsForCDS ( const objects::CSeq_feat &  fusedFeat, const objects::CSeq_feat &  feat_old  )

private

Merges protein sequence features for duplicate coding regions.

Definition at line 1521 of file update_seq.cpp.

References CSeq_annot_EditHandle::AddFeat(), CSerialObject::Assign(), CBioseq_EditHandle::AttachAnnot(), CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetProduct(), ITERATE, m_OldBsh, NON_CONST_ITERATE, CSeq_annot_EditHandle::Remove(), CSeq_annot_Base::SetData(), and x_FuseFeatures().

Referenced by x_FuseFeatures().

x_GetNewAlign_Replace()

CConstRef< CSeq_align > CSequenceUpdater::x_GetNewAlign_Replace ( const objects::CBioseq_Handle &  bsh )

private

Definition at line 1409 of file update_seq.cpp.

References _ASSERT, CSerialObject::Assign(), ConstRef(), FindRowInAlignment(), CRef< C, Locker >::GetPointer(), m_Align, m_NewId, row, CDense_seg_Base::SetIds(), and CSeq_align_Base::SetSegs().

Referenced by NoChange(), and Replace().

x_GetNewSeqLength()

TSeqPos CSequenceUpdater::x_GetNewSeqLength ( )

private

Definition at line 623 of file update_seq.cpp.

References _ASSERT, FOR_EACH_SEQENTRY_ON_SEQSET, and m_NewEntry.

Referenced by x_MappedFeature_ThroughAlign(), and x_ReplaceIdInOldFeatures().

x_GetOldBseq_EntryHandle()

CSeq_entry_Handle CSequenceUpdater::x_GetOldBseq_EntryHandle ( void  )

private

Definition at line 1175 of file update_seq.cpp.

References _ASSERT, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetClass(), CBioseq_set_Handle::GetParentEntry(), CBioseq_set_Handle::IsSetClass(), and m_OldBsh.

Referenced by x_MakeNewEntry(), and x_SwapOldWithNewSeq().

x_GetSeqAnnot_WithoutCDS()

CRef< CSeq_annot > CSequenceUpdater::x_GetSeqAnnot_WithoutCDS ( bool &  has_cds )

private

Definition at line 1602 of file update_seq.cpp.

References CSeq_feat_Base::GetData(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), m_ImportUpdFeats, m_MappedOldFeats, NON_CONST_ITERATE, and CSeq_annot_Base::SetData().

Referenced by x_AttachFeaturesToNewSeq().

x_HandleDuplicateFeatures()

void CSequenceUpdater::x_HandleDuplicateFeatures ( )

private

Decides which duplicate features will end up on the new sequence.

Definition at line 1427 of file update_seq.cpp.

References SUpdateSeqParams::eFeatUpdateAll, SUpdateSeqParams::eFeatUpdateAllExceptDups, SUpdateSeqParams::eFeatUpdateAllMergeDups, SUpdateSeqParams::eFeatUpdateAllReplaceDups, SUpdateSeqParams::m_FeatImportOption, m_ImportUpdFeats, m_MappedOldFeats, m_Params, and x_FuseFeatures().

Referenced by ExtendOneEndOfSequence(), NoChange(), Replace(), and x_MapOldAndImportedFeatsThroughNewAlign().

x_ImportCDSProduct()

void CSequenceUpdater::x_ImportCDSProduct ( CRef< objects::CSeq_feat >  cds, objects::CSeq_entry_EditHandle &  eh, objects::CBioseq_Handle &  newBsh, bool  create_general_only  )

private

Definition at line 1864 of file update_seq.cpp.

References CSerialObject::Assign(), CSeq_entry_EditHandle::AttachEntry(), CScope::GetBioseqHandle(), CSeq_entry_Handle::GetCompleteSeq_entry(), GetNewProtId(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_feat_Base::IsSetProduct(), SUpdateSeqParams::m_KeepProteinId, m_OldBsh, m_Params, offset, CScope::RemoveFromHistory(), CSeq_feat_Base::SetProduct(), x_RemoveDescriptorsFromImportedProducts(), and x_UpdateProteinID().

Referenced by x_AttachFeaturesToNewSeq().

x_MakeNewEntry()

void CSequenceUpdater::x_MakeNewEntry ( const objects::CSeq_inst &  newInst )

private

Creates the new seq-entry. It is not added to the scope, yet.

Definition at line 1133 of file update_seq.cpp.

References CSeq_entry_Handle::GetCompleteSeq_entry(), m_NewEntry, CRef< C, Locker >::Reset(), x_GetOldBseq_EntryHandle(), and x_PrepareNewEntry().

Referenced by ExtendOneEndOfSequence(), NoChange(), Patch(), and Replace().

x_MapOldAndImportedFeatsThroughNewAlign()

void CSequenceUpdater::x_MapOldAndImportedFeatsThroughNewAlign ( )

private

Definition at line 1101 of file update_seq.cpp.

References CSeqFeatData::eSubtype_any, FindRowInAlignment(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_ImportFeatures, m_ImportUpdFeats, m_MappedOldFeats, m_OldBsh, m_Params, m_UpdBsh, SAnnotSelector::SetLimitTSE(), x_ChangeIDInFeature(), x_FormNewAlignment(), x_HandleDuplicateFeatures(), x_MappedFeature_ThroughAlign(), and x_ShouldRemoveFeature().

Referenced by ExtendOneEndOfSequence(), and Patch().

x_MappedFeature_ChangeId()

CRef< CSeq_feat > CSequenceUpdater::x_MappedFeature_ChangeId ( const objects::CSeq_feat_Handle &  orig_fh )

private

Changes only the location ID of the feature.

Definition at line 1251 of file update_seq.cpp.

References CSeq_loc::Assign(), CSerialObject::Assign(), eExtreme_Biological, CSeqFeatData::eSubtype_tRNA, CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetSeq_feat(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CCdregion_Base::IsSetCode_break(), m_NewId, NON_CONST_ITERATE, CSeq_feat_Base::ResetLocation(), CSeq_feat_Base::ResetPartial(), rna, CCdregion_Base::SetCode_break(), CSeq_feat_Base::SetData(), CSeq_loc::SetId(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetPartial().

Referenced by Replace(), and x_ReplaceIdInOldFeatures().

x_MappedFeature_ThroughAlign()

CRef< CSeq_feat > CSequenceUpdater::x_MappedFeature_ThroughAlign ( const objects::CSeq_feat_Handle &  orig_fh, const objects::CSeq_align &  align  )

private

Maps feature's location through the alignment.

Definition at line 1296 of file update_seq.cpp.

References CSerialObject::Assign(), eExtreme_Biological, CSeqFeatData::eSubtype_tRNA, CSeq_inst_Base::eTopology_circular, CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetScope(), CSeq_feat_Handle::GetSeq_feat(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CCdregion_Base::IsSetCode_break(), m_NewId, m_OldBsh, NON_CONST_ITERATE, CSeq_feat_Base::ResetLocation(), CSeq_feat_Base::ResetPartial(), rna, CCdregion_Base::SetCode_break(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), and x_GetNewSeqLength().

Referenced by NoChange(), Replace(), and x_MapOldAndImportedFeatsThroughNewAlign().

x_PatchSequence()

CRef< CSeq_inst > CSequenceUpdater::x_PatchSequence ( )

private

Definition at line 818 of file update_seq.cpp.

References _ASSERT, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus, FindRowInAlignment(), CSeqVector::GetSeqData(), m_Align, m_OldBsh, m_UpdBsh, and x_UpdateSeqInst().

Referenced by Patch().

x_PrepareNewEntry()

void CSequenceUpdater::x_PrepareNewEntry ( CRef< objects::CSeq_entry >  entry, const objects::CSeq_inst &  newInst  )

private

Definition at line 1143 of file update_seq.cpp.

References CSeq_id::Assign(), CSeq_entry_Base::IsSeq(), m_NewEntry, m_NewId, CBioseq_Base::ResetAnnot(), CBioseq_set_Base::ResetAnnot(), CBioseq_Base::ResetId(), CBioseq_Base::ResetInst(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by x_MakeNewEntry().

x_PrintNewEntryIds()

void CSequenceUpdater::x_PrintNewEntryIds ( )

private

Definition at line 2080 of file update_seq.cpp.

References _ASSERT, FOR_EACH_SEQENTRY_ON_SEQSET, Info(), LOG_POST, m_NewEntry, and MSerial_AsnText.

x_RemoveDescriptorsFromImportedProducts()

void CSequenceUpdater::x_RemoveDescriptorsFromImportedProducts ( CRef< objects::CSeq_entry >  protein )

private

Removes RefGeneTracking user-object and create-date descriptors from imported cds products.

Definition at line 1939 of file update_seq.cpp.

References CSeqdesc_Base::e_Create_date, CSeqdesc_Base::e_User, EDIT_EACH_SEQDESC_ON_SEQDESCR, NStr::EqualCase(), ERASE_SEQDESC_ON_SEQDESCR, CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_object_Base::IsSetClass(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and CSeq_entry::SetDescr().

Referenced by x_ImportCDSProduct(), and x_RetranslateImportedCDSProduct().

x_RemoveNewIDInFeature()

void CSequenceUpdater::x_RemoveNewIDInFeature ( CRef< objects::CSeq_feat >  feat )

private

Definition at line 1906 of file update_seq.cpp.

References _ASSERT, CSeq_id::Assign(), CSeq_id::BestRank(), CSeqFeatData::eSubtype_tRNA, FindBestChoice(), CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsCdregion(), CCdregion_Base::IsSetCode_break(), m_OldBsh, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), rna, CCdregion_Base::SetCode_break(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by x_SetOldIDInFeatures().

x_ReplaceIdInOldFeatures()

void CSequenceUpdater::x_ReplaceIdInOldFeatures ( )

private

Definition at line 1076 of file update_seq.cpp.

References eExtreme_Positional, CSeqFeatData::eSubtype_any, m_MappedOldFeats, m_OldBsh, SAnnotSelector::SetLimitTSE(), CSeq_feat_Base::SetLocation(), x_GetNewSeqLength(), x_MappedFeature_ChangeId(), and x_ShouldRemoveFeature().

Referenced by NoChange(), and Replace().

x_ReplaceSequence()

CRef< CSeq_inst > CSequenceUpdater::x_ReplaceSequence ( )

private

Definition at line 775 of file update_seq.cpp.

References CSerialObject::Assign(), CSeq_data_Base::e_Iupacna, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CSeqVector::GetSeqData(), m_OldBsh, m_UpdBsh, NCBI_THROW, CSeqportUtil::Pack(), CSeq_inst_Base::ResetExt(), CUpdateSeq_Input::s_IsDeltaWithNoGaps(), CSeqVector::SetCoding(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), and CSeq_inst_Base::SetSeq_data().

Referenced by Replace().

x_RetranslateImportedCDSProduct()

void CSequenceUpdater::x_RetranslateImportedCDSProduct ( CRef< objects::CSeq_feat >  cds, objects::CSeq_entry_EditHandle &  eh, objects::CBioseq_Handle &  newBsh, bool  create_general_only  )

private

Definition at line 1813 of file update_seq.cpp.

References CSerialObject::Assign(), CSeq_entry_EditHandle::AttachEntry(), CreateTranslatedProteinSequence(), eExtreme_Biological, NStr::Find(), CScope::GetBioseqHandle(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::GetLocation(), GetNewProtId(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetProduct(), SUpdateSeqParams::m_KeepProteinId, m_OldBsh, m_Params, offset, CScope::RemoveFromHistory(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetLength(), SetMolinfoForProtein(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CSeq_inst_Base::SetSeq_data(), x_AdjustProteinFeature(), and x_RemoveDescriptorsFromImportedProducts().

Referenced by x_AttachFeaturesToNewSeq().

x_RetranslateOldCDSProduct()

void CSequenceUpdater::x_RetranslateOldCDSProduct ( CRef< objects::CSeq_feat >  cds, objects::CSeq_entry_EditHandle &  eh, objects::CBioseq_Handle &  newBsh, bool  create_general_only  )

private

Definition at line 1753 of file update_seq.cpp.

References CSerialObject::Assign(), CSeq_entry_EditHandle::AttachEntry(), CreateTranslatedProteinSequence(), eExtreme_Biological, NStr::Find(), CScope::GetBioseqHandle(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetProduct(), m_OldBsh, CBioseq_Base::SetInst(), CSeq_inst_Base::SetLength(), SetMolinfoForProtein(), CSeq_entry_Base::SetSeq(), CSeq_inst_Base::SetSeq_data(), and x_AdjustProteinFeature().

Referenced by x_AttachFeaturesToNewSeq().

x_SetOldIDInFeatures()

void CSequenceUpdater::x_SetOldIDInFeatures ( )

private

Definition at line 1637 of file update_seq.cpp.

References m_ImportUpdFeats, m_MappedOldFeats, NON_CONST_ITERATE, and x_RemoveNewIDInFeature().

Referenced by x_AttachFeaturesToNewSeq().

x_ShouldImportFeature()

bool CSequenceUpdater::x_ShouldImportFeature ( const objects::CSeq_feat_Handle &  fh )

private

Determines whether the feature from update sequence should be imported to the new one.

Definition at line 1196 of file update_seq.cpp.

References _ASSERT, Compare(), eAbutting, eNoOverlap, fCompareOverlapping, FindRowInAlignment(), CSeq_feat_Base::GetData(), CSeq_loc::GetLabel(), CSeq_feat_Base::GetLocation(), CSeq_feat_Handle::GetOriginalSeq_feat(), CSeqFeatData::GetSubtype(), label, m_Align, SUpdateSeqParams::m_IgnoreAlignment, m_NotImportedFeats, m_Params, m_UpdBsh, and CSeqFeatData::SubtypeValueToName().

Referenced by NoChange().

x_ShouldRemoveFeature()

bool CSequenceUpdater::x_ShouldRemoveFeature ( const objects::CSeq_feat_Handle &  fh )

private

Definition at line 1221 of file update_seq.cpp.

References _ASSERT, eExtreme_Positional, SUpdateSeqParams::eFeatRemoveAligned, SUpdateSeqParams::eFeatRemoveAll, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatRemoveNotAligned, FindRowInAlignment(), CSeq_feat_Handle::GetLocation(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), m_Align, SUpdateSeqParams::m_FeatRemoveOption, m_OldBsh, and m_Params.

Referenced by ExtendOneEndOfSequence(), Replace(), x_MapOldAndImportedFeatsThroughNewAlign(), and x_ReplaceIdInOldFeatures().

x_SwapOldWithNewSeq()

CIRef< IEditCommand > CSequenceUpdater::x_SwapOldWithNewSeq ( )

private

Creates command that swaps the old sequence with the new one.

Definition at line 2072 of file update_seq.cpp.

References cmd, m_NewEntry, and x_GetOldBseq_EntryHandle().

Referenced by Update().

x_UpdateProteinID()

void CSequenceUpdater::x_UpdateProteinID ( CRef< objects::CSeq_entry >  protein, CRef< objects::CSeq_id >  newId  )

private

Definition at line 2014 of file update_seq.cpp.

References EDIT_EACH_FEATURE_ON_ANNOT, EDIT_EACH_SEQANNOT_ON_BIOSEQ, CSeq_entry_Base::GetSeq(), CSeq_annot::IsFtable(), CBioseq::IsNa(), CSeq_entry_Base::IsSet(), CBioseq_Base::ResetId(), CBioseq_Base::SetId(), and CSeq_entry_Base::SetSeq().

Referenced by x_ImportCDSProduct().

x_UpdateSeqInst()

CRef< CSeq_inst > CSequenceUpdater::x_UpdateSeqInst ( const string &  upd_str )

private

Definition at line 983 of file update_seq.cpp.

References m_OldBsh, and s_UpdateSeqInst().

Referenced by x_ExtendOneEnd(), and x_PatchSequence().

Member Data Documentation

m_Align

CConstRef<objects::CSeq_align> CSequenceUpdater::m_Align

private

Definition at line 200 of file update_seq.hpp.

Referenced by CheckParameters(), GetNotImportedFeatsReport(), IsAlignmentOK(), NoChange(), Patch(), Replace(), Update(), x_ExtendOneEnd(), x_GetNewAlign_Replace(), x_PatchSequence(), x_ShouldImportFeature(), and x_ShouldRemoveFeature().

m_CitSubMessage

string CSequenceUpdater::m_CitSubMessage

private

Definition at line 216 of file update_seq.hpp.

Referenced by GetCitSubMessage(), ShowCitSubMessage(), and x_AddCitSubToUpdatedSequence().

m_ImportUpdFeats

TFeatList CSequenceUpdater::m_ImportUpdFeats

private

Definition at line 213 of file update_seq.hpp.

Referenced by ExtendOneEndOfSequence(), NoChange(), Replace(), x_AttachFeaturesToNewSeq(), x_GetSeqAnnot_WithoutCDS(), x_HandleDuplicateFeatures(), x_MapOldAndImportedFeatsThroughNewAlign(), and x_SetOldIDInFeatures().

m_MappedOldFeats

TFeatList CSequenceUpdater::m_MappedOldFeats

private

List of features, originally belonging to the Old Sequence and update sequence, respectively.

Their locations have been adjusted (including new SeqId), ready to be attached to the New Sequence Lists are ready to be searched for duplicates

Definition at line 212 of file update_seq.hpp.

Referenced by ExtendOneEndOfSequence(), Replace(), x_AttachFeaturesToNewSeq(), x_GetSeqAnnot_WithoutCDS(), x_HandleDuplicateFeatures(), x_MapOldAndImportedFeatsThroughNewAlign(), x_ReplaceIdInOldFeatures(), and x_SetOldIDInFeatures().

m_NewEntry

CRef<objects::CSeq_entry> CSequenceUpdater::m_NewEntry

private

The new seq-entry.

Definition at line 204 of file update_seq.hpp.

Referenced by x_AddCitSubToUpdatedSequence(), x_AttachFeaturesToNewSeq(), x_FixID_AttachFeatures(), x_FixIDInNewEntry(), x_FormNewAlignment(), x_GetNewSeqLength(), x_MakeNewEntry(), x_PrepareNewEntry(), x_PrintNewEntryIds(), and x_SwapOldWithNewSeq().

m_NewId

CConstRef<objects::CSeq_id> CSequenceUpdater::m_NewId

private

Temporary seq-id of the new seq-entry.

Definition at line 206 of file update_seq.hpp.

Referenced by ExtendOneEndOfSequence(), Update(), x_FormNewAlignment(), x_GetNewAlign_Replace(), x_MappedFeature_ChangeId(), x_MappedFeature_ThroughAlign(), and x_PrepareNewEntry().

m_NotImportedFeats

vector<string> CSequenceUpdater::m_NotImportedFeats

private

List of features that were not imported as they were outside the alignment range.

Definition at line 219 of file update_seq.hpp.

Referenced by GetNotImportedFeatsReport(), and x_ShouldImportFeature().

m_OldBsh

objects::CBioseq_Handle CSequenceUpdater::m_OldBsh

private

Definition at line 198 of file update_seq.hpp.

Referenced by ExtendOneEndOfSequence(), GetRevCompReport(), IsOldSequenceOK(), NoChange(), Replace(), x_AddCitSubToUpdatedSequence(), x_AdjustOldCDSProduct(), x_AttachFeaturesToNewSeq(), x_ExtendOneEnd(), x_FixIDInNewEntry(), x_FormNewAlignment(), x_FuseProtFeatsForCDS(), x_GetOldBseq_EntryHandle(), x_ImportCDSProduct(), x_MapOldAndImportedFeatsThroughNewAlign(), x_MappedFeature_ThroughAlign(), x_PatchSequence(), x_RemoveNewIDInFeature(), x_ReplaceIdInOldFeatures(), x_ReplaceSequence(), x_RetranslateImportedCDSProduct(), x_RetranslateOldCDSProduct(), x_ShouldRemoveFeature(), and x_UpdateSeqInst().

m_Params

SUpdateSeqParams CSequenceUpdater::m_Params

private

Definition at line 201 of file update_seq.hpp.

Referenced by CheckParameters(), ExtendOneEndOfSequence(), NoChange(), Replace(), SetUpdateSeqParams(), Update(), x_AttachFeaturesToNewSeq(), x_ExtendOneEnd(), x_HandleDuplicateFeatures(), x_ImportCDSProduct(), x_MapOldAndImportedFeatsThroughNewAlign(), x_RetranslateImportedCDSProduct(), x_ShouldImportFeature(), and x_ShouldRemoveFeature().

m_Reversed

bool CSequenceUpdater::m_Reversed

private

Definition at line 217 of file update_seq.hpp.

Referenced by GetRevCompReport(), IsReverseComplemented(), and Update().

m_UpdBsh

const objects::CBioseq_Handle& CSequenceUpdater::m_UpdBsh

private

Definition at line 199 of file update_seq.hpp.

Referenced by CSequenceUpdater(), ExtendOneEndOfSequence(), GetNotImportedFeatsReport(), IsUpdateSequenceRaw(), NoChange(), Replace(), x_ExtendOneEnd(), x_MapOldAndImportedFeatsThroughNewAlign(), x_PatchSequence(), x_ReplaceSequence(), and x_ShouldImportFeature().

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

• include/gui/packages/pkg_sequence_edit/update_seq.hpp
• src/gui/packages/pkg_sequence_edit/update_seq.cpp