cuSequence.cpp File Reference

#include <ncbi_pch.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/NCBIeaa.hpp>
#include <objects/seq/IUPACaa.hpp>
#include <objects/seq/NCBIstdaa.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/seqblock/PDB_block.hpp>
#include <objects/seqloc/Giimport_id.hpp>
#include <objects/seqloc/Patent_seq_id.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/id1/id1_client.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <algo/structure/cd_utils/cuSequence.hpp>
#include <algo/structure/cd_utils/cuDbPriority.hpp>

Include dependency graph for cuSequence.cpp:

Go to the source code of this file.

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Functions
bool	SeqIdsMatch (const CRef< CSeq_id > &ID1, const CRef< CSeq_id > &ID2)
bool	SeqIdHasMatchInBioseq (const CRef< CSeq_id > &id, const CBioseq &bioseq)
int	GetCDDPssmIdFromSeqId (const CRef< CSeq_id > &id)
int	GetMMDBId (const CBioseq &bioseq)
TTaxId	GetTaxIdInBioseq (const CBioseq &bioseq)
bool	IsEnvironmentalSeq (const CBioseq &bioseq)
string	GetSpeciesFromBioseq (const CBioseq &bioseq)
int	GetSeqLength (const CBioseq &bioseq)
bool	GetSeqLength (const CRef< CSeq_entry > &Seq, int &len)
void	NcbistdaaToNcbieaaString (const std::vector< char > &vec, std::string *str)
bool	NcbieaaToNcbistdaaString (const std::string &str, vector< char > &vec)
bool	GetNcbieaaString (const CRef< CSeq_entry > &Seq, string &Str)
bool	GetNcbieaaString (const CBioseq &bioseq, string &Str)
bool	GetNcbistdSeq (const CBioseq &bioseq, vector< char > &seqData)
string	GetRawSequenceString (const CBioseq &bioseq)
char	GetResidueAtPosition (const CRef< CSeq_entry > &seqEntry, int pos, bool zeroBased)
char	GetResidueAtPosition (const CBioseq &bioseq, int pos, bool zeroBased)
bool	IsConsensus (const CRef< CSeq_id > &seqId)
bool	GetAccAndVersion (const CRef< CBioseq > bioseq, string &acc, int &version, CRef< CSeq_id > &seqId)
bool	GetPDBBlockFromSeqEntry (CRef< CSeq_entry > seqEntry, CRef< CPDB_block > &pdbBlock)
bool	CopyGiSeqId (const CRef< CBioseq > &bioseq, CRef< CSeq_id > &giSeqId, unsigned int nth)
bool	ExtractGi (const CRef< CBioseq > &bioseq, TGi &gi, unsigned int nth)
bool	CopyPdbSeqId (const CRef< CBioseq > &bioseq, CRef< CSeq_id > &pdbSeqId, unsigned int nth)
bool	ExtractPdbMolChain (const CRef< CBioseq > &bioseq, string &pdbMol, string &pdbChain, unsigned int nth)
bool	HasSeqIdOfType (const CBioseq &bioseq, CSeq_id::E_Choice choice)
bool	HasSeqIdOfType (const CRef< CSeq_entry > &seqEntry, CSeq_id::E_Choice choice)
unsigned int	CopySeqIdsOfType (const CBioseq &bioseq, CSeq_id::E_Choice choice, list< CRef< CSeq_id > > &idsOfType)
unsigned int	CopySeqIdsOfType (const CRef< CSeq_entry > &seqEntry, CSeq_id::E_Choice choice, list< CRef< CSeq_id > > &idsOfType)
bool	CopyBioseqWithType (const CRef< CSeq_entry > &seqEntry, CSeq_id::E_Choice choice, CRef< CBioseq > &seqEntryBioseq)
bool	GetBioseqWithType (CRef< CSeq_entry > &seqEntry, CSeq_id::E_Choice choice, CRef< CBioseq > &seqEntryBioseq)
bool	AddCommentToBioseq (CBioseq &bioseq, const string &comment)
void	SimplifyBioseqForCD (CBioseq &bioseq, const vector< string > &keptComments, bool keepPDBBlock)
void	SimplifySeqEntryForCD (CRef< CSeq_entry > &seqEntry, const vector< string > &keptComments, bool keepPDBBlock)
string	GetDbSourceForSeqId (const CRef< CSeq_id > &seqID)
string	GetAccessionForSeqId (const CRef< CSeq_id > &seqID)
void	GetAccessionAndDatabaseSource (const CRef< CSeq_id > &seqID, string &accession, string &dbSource, bool getGenericSource)
bool	extractBioseqInfo (const CRef< CBioseq > bioseq, BioseqInfo &info)

Function Documentation

AddCommentToBioseq()

bool AddCommentToBioseq	(	CBioseq &	bioseq,
		const string &	comment
	)

Definition at line 704 of file cuSequence.cpp.

References CBioseq_Base::IsSetDescr(), result, CSeq_descr_Base::Set(), CSeqdesc_Base::SetComment(), and CBioseq_Base::SetDescr().

CopyBioseqWithType()

bool CopyBioseqWithType	(	const CRef< CSeq_entry > &	seqEntry,
		CSeq_id::E_Choice	choice,
		CRef< CBioseq > &	seqEntryBioseq
	)

Definition at line 640 of file cuSequence.cpp.

References CSerialObject::Assign(), CopySeqIdsOfType(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CRef< C, Locker >::NotEmpty(), and result.

CopyGiSeqId()

bool CopyGiSeqId	(	const CRef< CBioseq > &	bioseq,
		CRef< CSeq_id > &	giSeqId,
		unsigned int	nth
	)

Definition at line 487 of file cuSequence.cpp.

References CSeq_id::Assign(), CBioseq_Base::GetId(), and result.

Referenced by ExtractGi().

CopyPdbSeqId()

bool CopyPdbSeqId	(	const CRef< CBioseq > &	bioseq,
		CRef< CSeq_id > &	pdbSeqId,
		unsigned int	nth
	)

Definition at line 522 of file cuSequence.cpp.

References CSeq_id::Assign(), CBioseq_Base::GetId(), and result.

Referenced by ExtractPdbMolChain().

CopySeqIdsOfType() [1/2]

unsigned int CopySeqIdsOfType	(	const CBioseq &	bioseq,
		CSeq_id::E_Choice	choice,
		list< CRef< CSeq_id > > &	idsOfType
	)

Definition at line 595 of file cuSequence.cpp.

References CBioseq_Base::GetId().

Referenced by CopyBioseqWithType(), CopySeqIdsOfType(), and GetBioseqWithType().

CopySeqIdsOfType() [2/2]

unsigned int CopySeqIdsOfType	(	const CRef< CSeq_entry > &	seqEntry,
		CSeq_id::E_Choice	choice,
		list< CRef< CSeq_id > > &	idsOfType
	)

Definition at line 610 of file cuSequence.cpp.

References CopySeqIdsOfType(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), and CRef< C, Locker >::NotEmpty().

extractBioseqInfo()

bool extractBioseqInfo	(	const CRef< CBioseq >	bioseq,
		BioseqInfo &	info
	)

Definition at line 889 of file cuSequence.cpp.

References CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::CanGetVersion(), CSeq_descr_Base::Get(), CTextseq_id_Base::GetAccession(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CTextseq_id_Base::GetVersion(), info, and CBioseq_Base::IsSetDescr().

ExtractGi()

bool ExtractGi	(	const CRef< CBioseq > &	bioseq,
		TGi &	gi,
		unsigned int	nth
	)

Definition at line 508 of file cuSequence.cpp.

References CopyGiSeqId(), CSeq_id_Base::GetGi(), result, and ZERO_GI.

ExtractPdbMolChain()

bool ExtractPdbMolChain	(	const CRef< CBioseq > &	bioseq,
		string &	pdbMol,
		string &	pdbChain,
		unsigned int	nth
	)

Definition at line 544 of file cuSequence.cpp.

References CopyPdbSeqId(), CAliasBase< TPrim >::Get(), CPDB_seq_id::GetEffectiveChain_id(), CPDB_seq_id_Base::GetMol(), CSeq_id_Base::GetPdb(), and result.

GetAccAndVersion()

bool GetAccAndVersion	(	const CRef< CBioseq >	bioseq,
		string &	acc,
		int &	version,
		CRef< CSeq_id > &	seqId
	)

Definition at line 420 of file cuSequence.cpp.

References CSeq_id::Assign(), CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::CanGetVersion(), CTextseq_id_Base::GetAccession(), CBioseq_Base::GetId(), CTextseq_id_Base::GetVersion(), and dtl::version.

Referenced by CDRefresher::addSequence(), CDUpdater::findRowsWithOldSeq(), CDRefresher::hasOlderVersion(), and CDRefresher::refresh().

GetAccessionAndDatabaseSource()

void GetAccessionAndDatabaseSource	(	const CRef< CSeq_id > &	seqID,
		string &	accession,
		string &	dbSource,
		bool	getGenericSource
	)

Definition at line 811 of file cuSequence.cpp.

References CTextseq_id_Base::CanGetAccession(), CGiimport_id_Base::CanGetDb(), CTextseq_id_Base::CanGetName(), CCdDbPriority::eDPUnknown, CAliasBase< TPrim >::Get(), CTextseq_id_Base::GetAccession(), CDbtag_Base::GetDb(), CGiimport_id_Base::GetDb(), CPDB_seq_id::GetEffectiveChain_id(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CObject_id_Base::GetId(), CGiimport_id_Base::GetId(), CSeq_id_Base::GetLocal(), CPDB_seq_id_Base::GetMol(), CTextseq_id_Base::GetName(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CPatent_seq_id_Base::GetSeqid(), CCdDbPriority::GetSourceName(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CSeq_id::GetTextseq_Id(), NStr::IntToString(), CSeq_id_Base::IsGeneral(), CSeq_id_Base::IsGi(), CSeq_id_Base::IsGibbmt(), CSeq_id_Base::IsGibbsq(), CSeq_id_Base::IsGiim(), CObject_id_Base::IsId(), CSeq_id_Base::IsLocal(), CSeq_id_Base::IsPatent(), CSeq_id_Base::IsPdb(), CDbtag_Base::IsSetDb(), CDbtag_Base::IsSetTag(), CObject_id_Base::IsStr(), NStr::NumericToString(), CCdDbPriority::SeqIdTypeToSource(), and CSeq_id_Base::Which().

Referenced by GetAccessionForSeqId(), and GetDbSourceForSeqId().

GetAccessionForSeqId()

string GetAccessionForSeqId

(

const CRef< CSeq_id > &

seqID

)

Definition at line 803 of file cuSequence.cpp.

References GetAccessionAndDatabaseSource().

GetBioseqWithType()

bool GetBioseqWithType	(	CRef< CSeq_entry > &	seqEntry,
		CSeq_id::E_Choice	choice,
		CRef< CBioseq > &	seqEntryBioseq
	)

Definition at line 672 of file cuSequence.cpp.

References CopySeqIdsOfType(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CRef< C, Locker >::NotEmpty(), result, CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

GetCDDPssmIdFromSeqId()

int GetCDDPssmIdFromSeqId

(

const CRef< CSeq_id > &

id

)

Definition at line 97 of file cuSequence.cpp.

References database, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CDbtag_Base::GetTag(), CSeq_id_Base::IsGeneral(), and CObject_id_Base::IsId().

Referenced by GetPssmIdFromSeqAlign().

GetDbSourceForSeqId()

string GetDbSourceForSeqId

(

const CRef< CSeq_id > &

seqID

)

Definition at line 796 of file cuSequence.cpp.

References GetAccessionAndDatabaseSource().

GetMMDBId()

int GetMMDBId

(

const CBioseq &

bioseq

)

Definition at line 112 of file cuSequence.cpp.

References CBioseq_Base::GetAnnot(), and CBioseq_Base::IsSetAnnot().

Referenced by CCdCore::GetMmdbId(), and AlignmentCollection::IsStruct().

GetNcbieaaString() [1/2]

bool GetNcbieaaString	(	const CBioseq &	bioseq,
		string &	Str
	)

Definition at line 298 of file cuSequence.cpp.

References CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacaa(), CSeq_data_Base::GetNcbieaa(), CSeq_data_Base::GetNcbistdaa(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_data_Base::IsNcbistdaa(), CSeq_inst_Base::IsSetSeq_data(), and NcbistdaaToNcbieaaString().

Referenced by AlignmentCollection::GetSequenceForRow(), CCdCore::GetSequenceStringByIndex(), CDRefresher::refresh(), and CdBlaster::truncateBioseq().

GetNcbieaaString() [2/2]

bool GetNcbieaaString	(	const CRef< CSeq_entry > &	Seq,
		string &	Str
	)

Definition at line 289 of file cuSequence.cpp.

References CBioseq_Base::GetInst(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::IsSeq(), and CSeq_inst_Base::IsSetSeq_data().

Referenced by GetResidueAtPosition().

GetNcbistdSeq()

bool GetNcbistdSeq	(	const CBioseq &	bioseq,
		vector< char > &	seqData
	)

Definition at line 315 of file cuSequence.cpp.

References CSeqConvert::Convert(), CSeqUtil::e_Iupacaa, CSeqUtil::e_Ncbieaa, CSeqUtil::e_Ncbistdaa, CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacaa(), CSeq_data_Base::GetNcbieaa(), CSeq_data_Base::GetNcbistdaa(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_data_Base::IsNcbistdaa(), and CSeq_inst_Base::IsSetSeq_data().

Referenced by PssmScorer::score().

GetPDBBlockFromSeqEntry()

bool GetPDBBlockFromSeqEntry	(	CRef< CSeq_entry >	seqEntry,
		CRef< CPDB_block > &	pdbBlock
	)

Definition at line 446 of file cuSequence.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_set_Base::GetDescr(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CRef< C, Locker >::Reset(), and CSeqdesc_Base::SetPdb().

Referenced by CDUpdater::reformatBioseq().

GetRawSequenceString()

string GetRawSequenceString

(

const CBioseq &

bioseq

)

Definition at line 349 of file cuSequence.cpp.

References CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacaa(), CSeq_data_Base::GetNcbieaa(), CSeq_data_Base::GetNcbistdaa(), CSeq_inst_Base::GetSeq_data(), i, int, CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_data_Base::IsNcbistdaa(), CSeq_inst_Base::IsSetSeq_data(), and kEmptyStr.

Referenced by CDUpdater::update().

GetResidueAtPosition() [1/2]

char GetResidueAtPosition	(	const CBioseq &	bioseq,
		int	pos,
		bool	zeroBased
	)

Definition at line 389 of file cuSequence.cpp.

References GetNcbieaaString(), and str().

GetResidueAtPosition() [2/2]

char GetResidueAtPosition	(	const CRef< CSeq_entry > &	seqEntry,
		int	pos,
		bool	zeroBased
	)

Definition at line 380 of file cuSequence.cpp.

References CBioseq_Base::GetInst(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::IsSeq(), and CSeq_inst_Base::IsSetSeq_data().

GetSeqLength() [1/2]

int GetSeqLength

(

const CBioseq &

bioseq

)

Definition at line 216 of file cuSequence.cpp.

References CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacaa(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbieaa(), CSeq_data_Base::GetNcbistdaa(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_data_Base::IsNcbistdaa(), CSeq_inst_Base::IsSetLength(), CSeq_inst_Base::IsSetSeq_data(), and len.

Referenced by GetSeqLength(), CDUpdater::isFragmentedSeq(), CSimpleB2SWrapper::SetSeq(), CWGSSeqIterator::x_AddQualityChunkInfo(), and CWGSSeqIterator::x_InitSplit().

GetSeqLength() [2/2]

bool GetSeqLength	(	const CRef< CSeq_entry > &	Seq,
		int &	len
	)

Definition at line 242 of file cuSequence.cpp.

References CRef< C, Locker >::Empty(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), GetSeqLength(), CSeq_entry_Base::IsSet(), CSeq_inst_Base::IsSetLength(), and len.

GetSpeciesFromBioseq()

string GetSpeciesFromBioseq

(

const CBioseq &

bioseq

)

Definition at line 190 of file cuSequence.cpp.

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

Referenced by CCdCore::GetSpeciesForIndex(), and CCdCore::GetSpeciesForRow().

GetTaxIdInBioseq()

TTaxId GetTaxIdInBioseq

(

const CBioseq &

bioseq

)

Definition at line 139 of file cuSequence.cpp.

References CSeq_descr_Base::Get(), COrg_ref_Base::GetDb(), CBioseq_Base::GetDescr(), CBioseq_Base::IsSetDescr(), NULL, TAX_ID_FROM, and ZERO_TAX_ID.

Referenced by GetCommonTax(), and IsEnvironmentalSeq().

HasSeqIdOfType() [1/2]

bool HasSeqIdOfType	(	const CBioseq &	bioseq,
		CSeq_id::E_Choice	choice
	)

Definition at line 559 of file cuSequence.cpp.

References CBioseq_Base::GetId(), and result.

Referenced by HasSeqIdOfType().

HasSeqIdOfType() [2/2]

bool HasSeqIdOfType	(	const CRef< CSeq_entry > &	seqEntry,
		CSeq_id::E_Choice	choice
	)

Definition at line 572 of file cuSequence.cpp.

References CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), HasSeqIdOfType(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CRef< C, Locker >::NotEmpty(), and result.

IsConsensus()

bool IsConsensus

(

const CRef< CSeq_id > &

seqId

)

Definition at line 405 of file cuSequence.cpp.

References CSeq_id_Base::GetLocal(), CObject_id_Base::GetStr(), CSeq_id_Base::IsLocal(), CObject_id_Base::IsStr(), CRef< C, Locker >::NotEmpty(), and result.

Referenced by ConsensusMaker::addRows(), ConsensusMaker::ConsensusMaker(), CCdCore::FindConsensusInSequenceList(), CCdCore::GetRowsWithConsensus(), CCdCore::HasConsensusSequence(), PssmMaker::printAlignment(), PssmMaker::printAlignmentByColumn(), PssmMaker::PssmMaker(), and CCdCore::UsesConsensusSequenceAsMaster().

IsEnvironmentalSeq()

bool IsEnvironmentalSeq

(

const CBioseq &

bioseq

)

Definition at line 184 of file cuSequence.cpp.

References ENVIRONMENTAL_SEQUENCE_TAX_ID, and GetTaxIdInBioseq().

NcbieaaToNcbistdaaString()

bool NcbieaaToNcbistdaaString	(	const std::string &	str,
		vector< char > &	vec
	)

Definition at line 272 of file cuSequence.cpp.

References CSeqConvert::Convert(), CSeqUtil::e_Ncbieaa, CSeqUtil::e_Ncbistdaa, result, and str().

NcbistdaaToNcbieaaString()

void NcbistdaaToNcbieaaString	(	const std::vector< char > &	vec,
		std::string *	str
	)

Definition at line 258 of file cuSequence.cpp.

References CSeqConvert::Convert(), CSeqUtil::e_Ncbieaa, CSeqUtil::e_Ncbistdaa, and str().

Referenced by GetNcbieaaString().

SeqIdHasMatchInBioseq()

bool SeqIdHasMatchInBioseq	(	const CRef< CSeq_id > &	id,
		const CBioseq &	bioseq
	)

Definition at line 80 of file cuSequence.cpp.

References Empty(), CBioseq_Base::GetId(), result, and SeqIdsMatch().

Referenced by CCdCore::GetSeqIndex().

SeqIdsMatch()

bool SeqIdsMatch	(	const CRef< CSeq_id > &	ID1,
		const CRef< CSeq_id > &	ID2
	)

Definition at line 70 of file cuSequence.cpp.

Referenced by CheckSeqIdInDD(), CDUpdater::findSeq(), GetAlignedPositions(), CCdCore::GetNthMatchFor(), AlignmentCollection::GetRowsWithSeqID(), CCdCore::HasSeqId(), BlockModel::isAlike(), BlockModel::mask(), BlockModel::overlap(), CDUpdater::overlapWithCDRow(), BlockModelPair::remaster(), and SeqIdHasMatchInBioseq().

SimplifyBioseqForCD()

void SimplifyBioseqForCD	(	CBioseq &	bioseq,
		const vector< string > &	keptComments,
		bool	keepPDBBlock
	)

Definition at line 718 of file cuSequence.cpp.

References CPDB_block_Base::CanGetCompound(), CSeq_descr_Base::Get(), CPDB_block_Base::GetCompound(), CBioseq_Base::GetDescr(), CSeq_descr_Base::IsSet(), kEmptyStr, CBioseq_Base::ResetAnnot(), CBioseq_Base::ResetDescr(), CSeq_descr_Base::Set(), CBioseq_Base::SetDescr(), and CSeqdesc_Base::SetTitle().

Referenced by SimplifySeqEntryForCD().

SimplifySeqEntryForCD()

void SimplifySeqEntryForCD	(	CRef< CSeq_entry > &	seqEntry,
		const vector< string > &	keptComments,
		bool	keepPDBBlock
	)

Definition at line 778 of file cuSequence.cpp.

References CRef< C, Locker >::Empty(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and SimplifyBioseqForCD().