seq_entry_edit.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seq/Seq_gap.hpp>
#include <objects/seq/Linkage_evidence.hpp>
#include <objects/general/User_object.hpp>
#include <objects/submit/Seq_submit.hpp>

Include dependency graph for seq_entry_edit.hpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Typedefs
typedef vector< CSeq_entry_Handle >	TVecOfSeqEntryHandles
typedef pair< TSeqPos, int >	TLocAdjustment
typedef vector< TLocAdjustment >	TLocAdjustmentVector
typedef CRange< TSeqPos >	TRange
	A list of trim coordinates. More...
typedef vector< TRange >	TCuts

Enumerations
enum	EInternalTrimType { eTrimToClosestEnd = 0 , eTrimTo5PrimeEnd , eTrimTo3PrimeEnd , eDoNotTrimInternal }
	Any internal cut listed in TCuts will be converted to a terminal cut using one of these options. More...

Functions
void	AddSeqEntryToSeqEntry (const CSeq_entry_Handle &to, const CSeq_entry_Handle &add)
	Attach one Seq-entry to another. More...
void	AddBioseqToBioseq (const CBioseq_Handle &to, const CBioseq_Handle &add)
	Attach one Bioseq to another. More...
void	AddBioseqToBioseqSet (const CBioseq_set_Handle &bsst, const CBioseq_Handle &seq)
	Add a Bioseq to a Bioseq-set. More...
CRef< CSeq_entry >	SeqEntryFromSeqSubmit (const CSeq_submit &submit)
	Create a Seq-entry from a Seq-submit. More...
NCBI_XOBJEDIT_EXPORT void	SegregateSetsByBioseqList (const CSeq_entry_Handle &target, const CScope::TBioseqHandles &bioseq_handles)
	Split a Seq-entry, where the second part holds the given bioseqs. More...
void	DivvyUpAlignments (const TVecOfSeqEntryHandles &vecOfSeqEntryHandles)
	Call this if the alignments directly under these seq-entries are all jumbled up between each other. More...
void	BioseqSetDescriptorPropagateDown (const CBioseq_set_Handle &bioseq_set_h, const vector< CSeqdesc::E_Choice > &choices_to_delete=vector< CSeqdesc::E_Choice >())
	Moves descriptors down to children of the given bioseq-set. More...
void	BioseqSetDescriptorPropagateUp (CBioseq_set_Handle set)
	Moves descriptors up from children of the given bioseq-set if each child has an identical copy of the descriptor. More...
void	AddLocalIdUserObjects (CSeq_entry &entry)
	Creates a User-object descriptor on every sequence that has a local ID Contains the original local ID. More...
bool	HasRepairedIDs (const CSeq_entry &entry)
	Detects whether colliding IDs were fixed by comparing sequence IDs to the contents of the OriginalID User-object descriptor. More...
void	RemoveUserObjectType (CSeq_entry &entry, CUser_object::EObjectType type)
	Removes User-object descriptors of a certain type from the seq-entry. More...
void	HandleCollidingIds (CSeq_entry &entry)
void	ConvertRawToDeltaByNs (CSeq_inst &inst, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap=false, int gap_type=CSeq_gap::eType_unknown, int linkage=-1, int linkage_evidence=-1)
	ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to determine the gap location. More...
void	ConvertRawToDeltaByNs (CBioseq_Handle bsh, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap=false, int gap_type=CSeq_gap::eType_unknown, int linkage=-1, int linkage_evidence=-1)
TLocAdjustmentVector	NormalizeUnknownLengthGaps (CSeq_inst &inst, TSeqPos unknown_length=100)
	NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific length (100 by default). More...
void	SetLinkageType (CSeq_ext &ext, CSeq_gap::TType linkage_type)
	SetLinkageType A function to set the linkage_type for gaps in a delta sequence. More...
void	SetLinkageTypeScaffold (CSeq_ext &ext, CLinkage_evidence::TType evidence_type)
	SetLinkageTypeScaffold A special case of SetLinkageType. More...
void	SetLinkageTypeLinkedRepeat (CSeq_ext &ext, CLinkage_evidence::TType evidence_type)
void	AddLinkageEvidence (CSeq_ext &ext, CLinkage_evidence::TType evidence_type)
	AddLinkageEvidence A function to add linkage evidence for gaps in a delta sequence. More...
void	ResetLinkageEvidence (CSeq_ext &ext, CLinkage_evidence::TType evidence_type)
void	SortSeqDescr (CSeq_entry &entry)
void	SortSeqDescr (CSeq_descr &entry)
void	TrimSequenceAndAnnotation (CBioseq_Handle bsh, const TCuts &cuts, EInternalTrimType internal_cut_conversion=eTrimToClosestEnd)
	Trim sequence data and all associated annotation. More...
void	GetSortedCuts (CBioseq_Handle bsh, const TCuts &cuts, TCuts &sorted_cuts, EInternalTrimType internal_cut_conversion=eTrimToClosestEnd)
	1) Merge abutting and overlapping cuts. More...
void	TrimSeqData (CBioseq_Handle bsh, CRef< CSeq_inst > inst, const TCuts &sorted_cuts)
	Trim sequence data. More...
void	TrimSeqGraph (CBioseq_Handle bsh, CRef< CSeq_graph > graph, const TCuts &sorted_cuts)
	Trim Seq-graph annotation. More...
void	TrimSeqAlign (CBioseq_Handle bsh, CRef< CSeq_align > align, const TCuts &sorted_cuts)
	Trim Seq-align annotation. More...
void	TrimSeqFeat (CRef< CSeq_feat > feat, const TCuts &sorted_cuts, bool &bFeatureDeleted, bool &bFeatureTrimmed, bool &partial_start, bool &partial_stop)
	Trim Seq-feat annotation. More...
void	DeleteProteinAndRenormalizeNucProtSet (const CSeq_feat_Handle &feat_h)
	Secondary function needed after trimming Seq-feat. More...
NCBI_XOBJEDIT_EXPORT void	AdjustCdregionFrame (TSeqPos original_nuc_len, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)
	Secondary function needed after trimming Seq-feat. More...
CRef< CBioseq >	SetNewProteinSequence (CScope &new_scope, CRef< CSeq_feat > cds, CRef< CSeq_inst > new_inst)
	Secondary function needed after trimming Seq-feat. More...
void	RetranslateCdregion (CBioseq_Handle nuc_bsh, bool partial_start, bool partial_stop, CRef< CSeq_inst > trimmed_nuc_inst, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)
	Secondary function needed after trimming Seq-feat. More...
CRef< CSeqdesc >	FindUnverified (const CBioseq &seq)
bool	IsUnverifiedOrganism (const CBioseq &seq)
bool	IsUnverifiedFeature (const CBioseq &seq)
bool	IsUnverifiedMisassembled (const CBioseq &seq)
bool	IsUnverifiedContaminant (const CBioseq &seq)
string	GetTargetedLocusName (const CSeq_feat &feat)
string	GenerateTargetedLocusName (CBioseq_Handle seq)
void	SetTargetedLocusName (CBioseq_Handle seq, const string &tls)
string	GetTargetedLocusNameConsensus (const string &tls1, const string &tls2)

Typedef Documentation

TCuts

typedef vector<TRange> TCuts

Definition at line 221 of file seq_entry_edit.hpp.

TLocAdjustment

typedef pair<TSeqPos, int> TLocAdjustment

Definition at line 185 of file seq_entry_edit.hpp.

TLocAdjustmentVector

typedef vector<TLocAdjustment> TLocAdjustmentVector

Definition at line 186 of file seq_entry_edit.hpp.

TRange

typedef CRange<TSeqPos> TRange

A list of trim coordinates.

Definition at line 220 of file seq_entry_edit.hpp.

TVecOfSeqEntryHandles

typedef vector<CSeq_entry_Handle> TVecOfSeqEntryHandles

Definition at line 114 of file seq_entry_edit.hpp.

Enumeration Type Documentation

EInternalTrimType

enum EInternalTrimType

Any internal cut listed in TCuts will be converted to a terminal cut using one of these options.

The default is eTrimToClosestEnd.

Enumerator
eTrimToClosestEnd
eTrimTo5PrimeEnd
eTrimTo3PrimeEnd
eDoNotTrimInternal

Definition at line 225 of file seq_entry_edit.hpp.

Function Documentation

AddBioseqToBioseq()

void AddBioseqToBioseq	(	const CBioseq_Handle &	to,
		const CBioseq_Handle &	add
	)

Attach one Bioseq to another.

This function will add one Bioseq to another if: 1. 'to' is a nucleotide and 'add' is a protein. The result is a nuc-prot set contating both elements. 2. both Bioseqs have the same molecular type. The result is a segmented bioseq of which the two bioseqs serve as parts. 3. 'to' is a segmented bioseq and 'add' has the same molecular type as 'to'. 'add' will be added as a new part of 'to'.

Parameters

to	Bioseq to change
add	Bioseq to add

See also

AddSeqEntryToSeqEntry()

Definition at line 414 of file seq_entry_edit.cpp.

References CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst_Mol(), CSeq_inst::IsAa(), CSeq_inst::IsNa(), s_AddBioseqToBioseq(), and s_AddProtToNuc().

Referenced by AddSeqEntryToSeqEntry(), and s_AddBioseqToNucProtSet().

AddBioseqToBioseqSet()

void AddBioseqToBioseqSet	(	const CBioseq_set_Handle &	bsst,
		const CBioseq_Handle &	seq
	)

Add a Bioseq to a Bioseq-set.

This function will add the Bioseq to the set if: 1. The set is of class 'parts' and the Bioseq has the same molecular type as the other parts. 2.

Parameters

bsst	Bioseq to change
seq	Bioseq to add

See also

AddSeqEntryToSeqEntry()

Definition at line 469 of file seq_entry_edit.cpp.

References CBioseq_set_Base::eClass_conset, CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::eClass_equiv, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_gi, CBioseq_set_Base::eClass_gibb, CBioseq_set_Base::eClass_mut_set, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::eClass_other, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_pdb_entry, CBioseq_set_Base::eClass_phy_set, CBioseq_set_Base::eClass_pir, CBioseq_set_Base::eClass_pop_set, CBioseq_set_Base::eClass_pub_set, CBioseq_set_Base::eClass_segset, CBioseq_set_Base::eClass_swissprot, CBioseq_set_Base::eClass_wgs_set, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetEditHandle(), CBioseq_EditHandle::MoveTo(), s_AddBioseqToNucProtSet(), s_AddBioseqToPartsSet(), and s_AddBioseqToSegset().

Referenced by AddSeqEntryToSeqEntry().

AddLinkageEvidence()

void AddLinkageEvidence	(	CSeq_ext &	ext,
		CLinkage_evidence::TType	evidence_type
	)

AddLinkageEvidence A function to add linkage evidence for gaps in a delta sequence.

Note that this function will automatically set the linkage to eLinkage_linked.

Parameters

ext	The Seq_ext to adjust
evidence_type	The evidence type to use.

Returns

none

Definition at line 2040 of file seq_entry_edit.cpp.

References CSeq_gap::AddLinkageEvidence(), NON_CONST_ITERATE, CDelta_ext_Base::Set(), and CSeq_ext_Base::SetDelta().

AddLocalIdUserObjects()

void AddLocalIdUserObjects

(

CSeq_entry &

entry

)

Creates a User-object descriptor on every sequence that has a local ID Contains the original local ID.

Definition at line 1583 of file seq_entry_edit.cpp.

References CUser_object::eObjectType_OriginalId, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CUser_object_Base::IsSetData(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), ITERATE, MakeOriginalIdField(), NON_CONST_ITERATE, CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeqdesc_Base::SetUser().

Referenced by BOOST_AUTO_TEST_CASE(), HandleCollidingIds(), and TestCollidingAccessionFixes().

AddSeqEntryToSeqEntry()

void AddSeqEntryToSeqEntry	(	const CSeq_entry_Handle &	to,
		const CSeq_entry_Handle &	add
	)

Attach one Seq-entry to another.

Parameters

to	Seq-entry to change
add	Seq-entry to add

See also

Other forms of adding the content of one Seq-entry to another.

Definition at line 344 of file seq_entry_edit.cpp.

References AddBioseqToBioseq(), AddBioseqToBioseqSet(), CSeq_entry_Handle::GetSeq(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSeq(), and CSeq_entry_Handle::IsSet().

AdjustCdregionFrame()

NCBI_XOBJEDIT_EXPORT void AdjustCdregionFrame	(	TSeqPos	original_nuc_len,
		CRef< CSeq_feat >	cds,
		const TCuts &	sorted_cuts
	)

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then adjust cdregion frame.

Definition at line 3220 of file seq_entry_edit.cpp.

References CSeq_feat_Base::CanGetData(), CSeq_feat_Base::CanGetLocation(), eExtreme_Biological, eNa_strand_minus, eNa_strand_unknown, CSeqFeatData::eSubtype_cdregion, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStrand(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), and CSeq_feat_Base::SetData().

BioseqSetDescriptorPropagateDown()

void BioseqSetDescriptorPropagateDown	(	const CBioseq_set_Handle &	bioseq_set_h,
		const vector< CSeqdesc::E_Choice > &	choices_to_delete = vector< CSeqdesc::E_Choice >()
	)

Moves descriptors down to children of the given bioseq-set.

Each child gets a copy of all the descriptors. It does NOT check for duplicate Seqdescs.

Parameters

bioseq_set_h	This is the bioseq_set whose descriptors we're moving.
choices_to_delete	If non-empty, it indicates the types of CSeqdescs to delete instead of propagating.

Definition at line 1447 of file seq_entry_edit.cpp.

References CSeq_entry_EditHandle::AddDescr(), CSeqdesc_Base::e_not_set, CSeq_entry_CI::eNonRecursive, CBioseq_set_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CBioseq_set_Handle::GetParentEntry(), CBioseq_set_EditHandle::ResetDescr(), SerialClone(), CSeq_descr_Base::Set(), and CSeqdesc_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and s_PromoteSingletonSetsInSet().

BioseqSetDescriptorPropagateUp()

void BioseqSetDescriptorPropagateUp

(

CBioseq_set_Handle

set

)

Moves descriptors up from children of the given bioseq-set if each child has an identical copy of the descriptor.

It does NOT check for duplicate Seqdescs. Will not move molinfo, title, or source descriptors.

Parameters

bioseq_set_h

This is the bioseq_set whose descriptors we're moving.

Definition at line 1368 of file seq_entry_edit.cpp.

References CBioseq_set_EditHandle::AddSeqdesc(), CSerialObject::Assign(), first(), CSeq_descr_Base::Get(), CBioseq_set_Base::GetSeq_set(), CSeq_descr_Base::IsSet(), ITERATE, CBioseq_EditHandle::RemoveSeqdesc(), CBioseq_set_EditHandle::RemoveSeqdesc(), CSeq_descr_Base::Reset(), CSeq_descr_Base::Set(), CBioseq_EditHandle::SetDescr(), and CBioseq_set_EditHandle::SetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

ConvertRawToDeltaByNs() [1/2]

void ConvertRawToDeltaByNs	(	CBioseq_Handle	bsh,
		size_t	min_unknown,
		int	max_unknown,
		size_t	min_known,
		int	max_known,
		bool	is_assembly_gap = false,
		int	gap_type = CSeq_gap::eType_unknown,
		int	linkage = -1,
		int	linkage_evidence = -1
	)

Definition at line 1944 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), ConvertRawToDeltaByNs(), f(), FeatureAdjustForInsert(), FeatureAdjustForTrim(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), NormalizeUnknownLengthGaps(), CSeq_feat_EditHandle::Remove(), CSeq_feat_EditHandle::Replace(), and CBioseq_EditHandle::SetInst().

ConvertRawToDeltaByNs() [2/2]

void ConvertRawToDeltaByNs	(	CSeq_inst &	inst,
		size_t	min_unknown,
		int	max_unknown,
		size_t	min_known,
		int	max_known,
		bool	is_assembly_gap,
		int	gap_type,
		int	linkage,
		int	linkage_evidence
	)

ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to determine the gap location.

The size of the run of Ns determines whether a gap should be created and whether the gap should be of type known or unknown. Note that if the ranges overlap, unknown gaps will be preferred (allowing the user to create known length gaps for 20-forever, but unknown length gaps for 100, for example). Use a negative number for a maximum to indicate that there is no upper limit.

Parameters

inst	The Seq-inst to adjust
min_unknown	The minimum number of Ns to be converted to a gap of unknown length
max_unknown	The maximum number of Ns to be converted to a gap of unknown length
min_known	The minimum number of Ns to be converted to a gap of known length
max_known	The maximum number of Ns to be converted to a gap of known length

Returns

none

Definition at line 1804 of file seq_entry_edit.cpp.

References CSeqConvert::Convert(), CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeqUtil::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na, CSeq_data_Base::e_Ncbi8na, CSeqUtil::e_Ncbi8na, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacna(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbi2na(), CSeq_data_Base::GetNcbi4na(), CSeq_data_Base::GetNcbi8na(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::GetSeq_data(), CSeq_inst_Base::IsSetRepr(), CSeq_inst_Base::IsSetSeq_data(), ITERATE, CSeq_inst_Base::ResetSeq_data(), s_AddGap(), s_AddLiteral(), CSeq_inst_Base::SetRepr(), and CSeq_data_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), ConvertRawToDeltaByNs(), ConvertRawToDeltaByNsCommand_impl(), and ConvertRawToDeltaByNsHugeFileCmd_impl().

DeleteProteinAndRenormalizeNucProtSet()

void DeleteProteinAndRenormalizeNucProtSet

(

const CSeq_feat_Handle &

feat_h

)

Secondary function needed after trimming Seq-feat.

If the trim completely covers the feature (boolean reference bFeatureDeleted from TrimSeqFeat() returns true), then delete protein sequence and re-normalize nuc-prot set.

Definition at line 3177 of file seq_entry_edit.cpp.

References CSeq_entry_EditHandle::ConvertSetToSeq(), CSeqFeatData_Base::e_Cdregion, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetBioseq_setCore(), CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CSeq_feat_Handle::GetData(), CSeq_entry_Handle::GetEditHandle(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CMappedFeat::GetProduct(), CSeq_feat_Handle::GetScope(), CBioseq_set_Base::GetSeq_set(), CBioseq_set_Handle::IsEmptySeq_set(), CBioseq_Handle::IsProtein(), CBioseq_Handle::IsRemoved(), CBioseq_set_Handle::IsSetClass(), CSeq_feat_Handle::IsSetData(), CSeq_feat_Handle::IsSetProduct(), CBioseq_EditHandle::Remove(), CSeq_feat_EditHandle::Remove(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

DivvyUpAlignments()

void DivvyUpAlignments

(

const TVecOfSeqEntryHandles &

vecOfSeqEntryHandles

)

Call this if the alignments directly under these seq-entries are all jumbled up between each other.

It will move each Seq-align into the proper location. In particular, it looks at all the seq-ids in each seq-align. If none of them belong to any member of vecOfSeqEntryHandles, then that Seq-align is copied to all members of vecOfSeqEntryHandles. If it belongs to only one member of vecOfSeqEntryHandles, then it goes there. If the align belongs to more than one, it's destroyed.

Parameters

vecOfSeqEntryHandles

The Seq-entries we're considering for alignments.

Definition at line 1304 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CSeq_entry_EditHandle::AttachAnnot(), CSeq_entry_CI::eRecursive, CSeq_annot_CI::eSearch_entry, CSeq_entry_Handle::GetEditHandle(), ITERATE, and s_DivvyUpAlignments_ProcessAnnot().

Referenced by SegregateSetsByBioseqList().

FindUnverified()

CRef<CSeqdesc> FindUnverified

(

const CBioseq &

seq

)

Definition at line 3446 of file seq_entry_edit.cpp.

References CUser_object::eObjectType_Unverified, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), and CBioseq_Base::IsSetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

GenerateTargetedLocusName()

string GenerateTargetedLocusName

(

CBioseq_Handle

seq

)

Definition at line 3631 of file seq_entry_edit.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Rna, f(), CBioseq_Handle::GetScope(), and GetTargetedLocusName().

Referenced by CheckTargetedLocusEntry(), and CTLSContigHandler::ProcessBioseq().

GetSortedCuts()

void GetSortedCuts	(	CBioseq_Handle	bsh,
		const TCuts &	cuts,
		TCuts &	sorted_cuts,
		EInternalTrimType	internal_cut_conversion
	)

1) Merge abutting and overlapping cuts.

2) Adjust any internal cuts to terminal cuts according to option. 3) Sort the cuts from greatest to least so that sequence data and annotation will be deleted from greatest loc to smallest loc. That way we don't have to adjust coordinate values after each cut.

1) Merge abutting and overlapping cuts.

2) Merge abutting and overlapping cuts. 3) Sort the cuts from greatest to least so that sequence data and annotation will be deleted from greatest loc to smallest loc. That way we don't have to adjust coordinate values after each cut.

Definition at line 2405 of file seq_entry_edit.cpp.

References CRangeCmp::eAscending, CRangeCmp::eDescending, eDoNotTrimInternal, CBioseq_Handle::GetBioseqLength(), CRange_Base::GetFrom(), CRange_Base::GetTo(), s_AdjustInternalCutLocations(), s_MergeCuts(), and ct::sort().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

GetTargetedLocusName()

string GetTargetedLocusName

(

const CSeq_feat &

feat

)

Definition at line 3564 of file seq_entry_edit.cpp.

References CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, NStr::EqualNocase(), CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mobile_element, NStr::Find(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeqFeatData_Base::GetProt(), CSeq_feat_Base::GetQual(), CSeqFeatData_Base::GetRna(), CSeqFeatData::GetSubtype(), GetTargetedLocusName(), CSeq_feat_Base::IsSetComment(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetQual(), NStr::TruncateSpacesInPlace(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE().

GetTargetedLocusNameConsensus()

string GetTargetedLocusNameConsensus	(	const string &	tls1,
		const string &	tls2
	)

Definition at line 3690 of file seq_entry_edit.cpp.

References NStr::EndsWith(), NStr::Equal(), NStr::fSplit_Tokenize, i, NStr::IsBlank(), ITERATE, kEmptyStr, NStr::Split(), and NStr::StartsWith().

Referenced by BOOST_AUTO_TEST_CASE(), and CTLSContigHandler::ProcessBioseq().

HandleCollidingIds()

void HandleCollidingIds

(

CSeq_entry &

entry

)

Definition at line 1738 of file seq_entry_edit.cpp.

References AddLocalIdUserObjects(), CUser_object::eObjectType_OriginalId, HasRepairedIDs(), CSeq_entry::ReassignConflictingIds(), and RemoveUserObjectType().

Referenced by CObjectLoadingTask::AddObjects().

HasRepairedIDs()

bool HasRepairedIDs

(

const CSeq_entry &

entry

)

Detects whether colliding IDs were fixed by comparing sequence IDs to the contents of the OriginalID User-object descriptor.

Definition at line 1683 of file seq_entry_edit.cpp.

References CUser_object::eObjectType_OriginalId, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), HasRepairedIDs(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_Base::IsSetId(), CBioseq_set_Base::IsSetSeq_set(), and ITERATE.

Referenced by BOOST_AUTO_TEST_CASE(), s_CollidedIds(), and TestCollidingAccessionFixes().

IsUnverifiedContaminant()

bool IsUnverifiedContaminant

(

const CBioseq &

seq

)

Definition at line 3501 of file seq_entry_edit.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), and CBioseq_Base::IsSetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

IsUnverifiedFeature()

bool IsUnverifiedFeature

(

const CBioseq &

seq

)

Definition at line 3474 of file seq_entry_edit.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), and CBioseq_Base::IsSetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

IsUnverifiedMisassembled()

bool IsUnverifiedMisassembled

(

const CBioseq &

seq

)

Definition at line 3487 of file seq_entry_edit.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), and CBioseq_Base::IsSetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

IsUnverifiedOrganism()

bool IsUnverifiedOrganism

(

const CBioseq &

seq

)

Definition at line 3460 of file seq_entry_edit.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), and CBioseq_Base::IsSetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

NormalizeUnknownLengthGaps()

TLocAdjustmentVector NormalizeUnknownLengthGaps	(	CSeq_inst &	inst,
		TSeqPos	unknown_length
	)

NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific length (100 by default).

Parameters

inst	The Seq-inst to adjust

Returns

A vector of the adjustments to the sequence, which can be used to fix the locations of features on the sequence.

Definition at line 1907 of file seq_entry_edit.cpp.

References CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetRepr(), NON_CONST_ITERATE, CSeq_inst_Base::SetExt(), and CSeq_inst_Base::SetLength().

Referenced by CRawSeqToDeltaSeqByLoc::apply_impl(), BOOST_AUTO_TEST_CASE(), ConvertRawToDeltaByNs(), ConvertRawToDeltaByNsCommand_impl(), and ConvertRawToDeltaByNsHugeFileCmd_impl().

RemoveUserObjectType()

void RemoveUserObjectType	(	CSeq_entry &	entry,
		CUser_object::EObjectType	type
	)

Removes User-object descriptors of a certain type from the seq-entry.

Definition at line 1711 of file seq_entry_edit.cpp.

References EDIT_EACH_SEQDESC_ON_BIOSEQ, EDIT_EACH_SEQDESC_ON_SEQSET, ERASE_SEQDESC_ON_BIOSEQ, ERASE_SEQDESC_ON_SEQSET, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), CBioseq_Base::ResetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by BOOST_AUTO_TEST_CASE(), and HandleCollidingIds().

ResetLinkageEvidence()

void ResetLinkageEvidence	(	CSeq_ext &	ext,
		CLinkage_evidence::TType	evidence_type
	)

RetranslateCdregion()

void RetranslateCdregion	(	CBioseq_Handle	nuc_bsh,
		bool	isPartialStart,
		bool	isPartialStop,
		CRef< CSeq_inst >	trimmed_nuc_inst,
		CRef< CSeq_feat >	cds,
		const TCuts &	sorted_cuts
	)

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then retranslate cdregion.

Definition at line 3310 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CSeq_feat_Base::CanGetLocation(), CSeq_interval_Base::CanGetTo(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, eExtreme_Biological, eNa_strand_unknown, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_loc_Base::GetInt(), CBioseq::GetLength(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetOriginalFeature(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetScope(), CSeq_loc::GetStrand(), CSeq_loc_Base::IsInt(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_EditHandle::Replace(), CMolInfo_Base::SetBiomol(), CMolInfo_Base::SetCompleteness(), CBioseq_EditHandle::SetDescr(), CBioseq_EditHandle::SetInst(), CSeq_feat_Base::SetLocation(), CSeqdesc_Base::SetMolinfo(), SetNewProteinSequence(), SetPartial(), and CSeqFeatData_Base::Which().

Referenced by TrimSequenceAndAnnotation().

SegregateSetsByBioseqList()

NCBI_XOBJEDIT_EXPORT void SegregateSetsByBioseqList	(	const CSeq_entry_Handle &	target,
		const CScope::TBioseqHandles &	bioseq_handles
	)

Split a Seq-entry, where the second part holds the given bioseqs.

There are various complex rules here that may not be obvious at first glance.

Parameters

target	The Seq-entry to split
bioseq_handles	The array of bioseqs that should end up in the second part of the target, with the rest in the first part.

Definition at line 963 of file seq_entry_edit.cpp.

References DivvyUpAlignments(), CSeq_entry_CI::eNonRecursive, CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSet(), and s_MakeGroupsForUniqueValues().

SeqEntryFromSeqSubmit()

CRef<CSeq_entry> SeqEntryFromSeqSubmit

(

const CSeq_submit &

submit

)

Create a Seq-entry from a Seq-submit.

Parameters

submit

Seq-submit to create Seq-entry from

Definition at line 591 of file seq_entry_edit.cpp.

References AddSeqdescToBioseq(), AddSeqdescToSeqEntryRecursively(), CSerialObject::Assign(), CBioseq_set_Base::eClass_genbank, CSubmit_block_Base::GetCit(), CSeq_submit_Base::GetData(), CSeq_submit_Base::C_Data::GetEntrys(), CSeq_submit_Base::GetSub(), CSeq_submit::IsEntrys(), CSeq_entry_Base::IsSeq(), CSubmit_block_Base::IsSetCit(), CSeq_submit_Base::IsSetSub(), ITERATE, CBioseq_set_Base::SetClass(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CPub_Base::SetSub().

Referenced by BOOST_AUTO_TEST_CASE(), CLocalFileRestorer::x_AttachNewObject(), CUpdateSeq_Input::x_ReadUpdateSeq_ASN(), and CUpdateMultipleSeq_Input::x_ReadUpdateSeqs_ASN().

SetLinkageType()

void SetLinkageType	(	CSeq_ext &	ext,
		CSeq_gap::TType	linkage_type
	)

SetLinkageType A function to set the linkage_type for gaps in a delta sequence.

Parameters

ext	The Seq_ext to adjust
linkage_type	The linkage_type to use.

Returns

none

Definition at line 1990 of file seq_entry_edit.cpp.

References CSeq_gap::ChangeType(), NON_CONST_ITERATE, CDelta_ext_Base::Set(), and CSeq_ext_Base::SetDelta().

Referenced by BOOST_AUTO_TEST_CASE().

SetLinkageTypeLinkedRepeat()

void SetLinkageTypeLinkedRepeat	(	CSeq_ext &	ext,
		CLinkage_evidence::TType	evidence_type
	)

Definition at line 2021 of file seq_entry_edit.cpp.

References NON_CONST_ITERATE, CDelta_ext_Base::Set(), CSeq_ext_Base::SetDelta(), and CSeq_gap::SetLinkageTypeLinkedRepeat().

Referenced by BOOST_AUTO_TEST_CASE().

SetLinkageTypeScaffold()

void SetLinkageTypeScaffold	(	CSeq_ext &	ext,
		CLinkage_evidence::TType	evidence_type
	)

SetLinkageTypeScaffold A special case of SetLinkageType.

When type is Scaffold, linkage must be linked and linkage evidence must be provided.

Parameters

ext	The Seq_ext to adjust
evidence_type	The linkage_type to use.

Returns

none

Definition at line 2009 of file seq_entry_edit.cpp.

References NON_CONST_ITERATE, CDelta_ext_Base::Set(), CSeq_ext_Base::SetDelta(), and CSeq_gap::SetLinkageTypeScaffold().

SetNewProteinSequence()

CRef<CBioseq> SetNewProteinSequence	(	CScope &	new_scope,
		CRef< CSeq_feat >	cds,
		CRef< CSeq_inst >	new_inst
	)

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then make new protein sequence.

Definition at line 3280 of file seq_entry_edit.cpp.

References CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacaa(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbieaa(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_inst_Base::IsSetSeq_data(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetSeq_data(), and CSeqTranslator::TranslateToProtein().

Referenced by RetranslateCdregion().

SetTargetedLocusName()

void SetTargetedLocusName	(	CBioseq_Handle	seq,
		const string &	tls
	)

Definition at line 3659 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CUser_object::eObjectType_AutodefOptions, CBioseq_Handle::GetCompleteBioseq(), CAutoDefOptions::InitFromUserObject(), CBioseq_Base::IsSetDescr(), CAutoDefOptions::MakeUserObject(), NON_CONST_ITERATE, CBioseq_EditHandle::SetDescr(), CAutoDefOptions::SetTargetedLocusName(), and CSeqdesc_Base::SetUser().

Referenced by CTLSContigHandler::ProcessBioseq(), and CTLSMasterHandler::ProcessBioseq().

SortSeqDescr() [1/2]

void SortSeqDescr

(

CSeq_descr &

entry

)

Definition at line 3515 of file seq_entry_edit.cpp.

References CSeq_descr_Base::Set().

Referenced by SortSeqDescr().

SortSeqDescr() [2/2]

void SortSeqDescr

(

CSeq_entry &

entry

)

Definition at line 3520 of file seq_entry_edit.cpp.

References CSeq_entry_Base::IsSet(), CSeq_entry::IsSetDescr(), CSeq_entry::SetDescr(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and SortSeqDescr().

Referenced by CTbl2AsnApp::ProcessOneEntry(), and CTbl2AsnApp::ProcessSingleEntry().

TrimSeqAlign()

void TrimSeqAlign	(	CBioseq_Handle	bsh,
		CRef< CSeq_align >	align,
		const TCuts &	sorted_cuts
	)

Trim Seq-align annotation.

Definition at line 3037 of file seq_entry_edit.cpp.

References CDense_seg_Base::CanGetDim(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CBioseq_Handle::GetSeqId(), CDense_seg_Base::GetStarts(), CRange_Base::GetTo(), row, s_CutDensegSegment(), and CSeq_align_Base::SetSegs().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

TrimSeqData()

void TrimSeqData	(	CBioseq_Handle	bsh,
		CRef< CSeq_inst >	inst,
		const TCuts &	sorted_cuts
	)

Trim sequence data.

Definition at line 2502 of file seq_entry_edit.cpp.

References CScope::AddBioseq(), CSerialObject::Assign(), eNa_strand_plus, CSeq_inst_Base::eRepr_raw, CSeqMap::eSeqData, CSeqMap::fFindAny, CSeqMap::fIgnoreUnresolved, CBioseq_Handle::GetCompleteBioseq(), CSeq_inst_Base::GetLength(), CBioseq_Handle::GetScope(), CSeq_entry_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetTopLevelEntry(), CSeqMap_CI::GetType(), CBioseq_Handle::IsNucleotide(), CScope::RemoveBioseq(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), CSeqMap::ResolvedRangeIterator(), CAutoInitRef< T >::Set(), CSeq_inst_Base::SetExt(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), and UpdateSeqLength().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

TrimSeqFeat()

void TrimSeqFeat	(	CRef< CSeq_feat >	feat,
		const TCuts &	sorted_cuts,
		bool &	bFeatureDeleted,
		bool &	bFeatureTrimmed,
		bool &	partial_start,
		bool &	partial_stop
	)

Trim Seq-feat annotation.

Definition at line 3119 of file seq_entry_edit.cpp.

References CSeq_feat_Base::CanGetLocation(), CSeq_feat_Base::CanGetProduct(), eExtreme_Positional, eNa_strand_unknown, CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), GetStart(), GetStop(), CSeq_loc::GetStrand(), CRange_Base::GetTo(), s_SeqLocDelete(), CSeq_feat_Base::SetLocation(), SetPartial(), and CSeq_feat_Base::SetProduct().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

TrimSeqGraph()

void TrimSeqGraph	(	CBioseq_Handle	bsh,
		CRef< CSeq_graph >	graph,
		const TCuts &	sorted_cuts
	)

Trim Seq-graph annotation.

Definition at line 2820 of file seq_entry_edit.cpp.

References eExtreme_Positional, CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetLoc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CByte_graph_Base::GetValues(), CSeq_graph_Base::C_Graph::IsByte(), s_GetTrimCoordinates(), s_UpdateSeqGraphLoc(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetNumval(), and CByte_graph_Base::SetValues().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

TrimSequenceAndAnnotation()

void TrimSequenceAndAnnotation	(	CBioseq_Handle	bsh,
		const TCuts &	cuts,
		EInternalTrimType	internal_cut_conversion
	)

Trim sequence data and all associated annotation.

Trim sequence data and all associated annotation.

Definition at line 2147 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CDense_seg_Base::CanGetDim(), CDense_seg_Base::CanGetIds(), CSeq_inst_Base::CanGetLength(), CDense_seg_Base::CanGetLens(), CDense_seg_Base::CanGetNumseg(), CSeq_align_Base::CanGetSegs(), CDense_seg_Base::CanGetStarts(), NStr::CompareNocase(), DeleteProteinAndRenormalizeNucProtSet(), CSeq_annot_Base::C_Data::e_Align, CSeqFeatData_Base::e_Cdregion, CSeq_align_Base::C_Segs::e_Denseg, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_feat_Base::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_inst_Base::GetLength(), CMappedFeat::GetOriginalFeature(), CMappedGraph::GetOriginalGraph(), CAlign_CI::GetOriginalSeq_align(), CSeq_align_Base::GetSegs(), CAlign_CI::GetSeq_align_Handle(), CMappedGraph::GetSeq_graph_Handle(), GetSortedCuts(), CMappedGraph::GetTitle(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), CMappedGraph::IsSetTitle(), CSeq_align_Handle::Replace(), CSeq_feat_EditHandle::Replace(), CSeq_graph_Handle::Replace(), RetranslateCdregion(), s_BasicValidation(), s_GetRetainedRange(), CSeq_feat_Base::SetData(), CBioseq_EditHandle::SetInst(), TrimSeqAlign(), TrimSeqData(), TrimSeqFeat(), TrimSeqGraph(), CSeq_align_Base::C_Segs::Which(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE().