CDiscrepancyContext Class Reference

Search Toolkit Book for CDiscrepancyContext

#include "discrepancy_core.hpp"
(Private to src/misc/discrepancy.)

Inheritance diagram for CDiscrepancyContext:

Collaboration diagram for CDiscrepancyContext:

Classes
struct	CParseNode
struct	CRefNode
struct	CSeq_feat_run
struct	CSeq_feat_vec
struct	CSeqdesc_run
struct	CSeqdesc_vec

Public Types
enum	EFlag { eHasRearranged = 1 << 0 , eHasSatFeat = 1 << 1 , eHasNonSatFeat = 1 << 2 }
enum	EFixType { eFixNone , eFixSelf , eFixParent , eFixSet }
	BIG FILE. More...
Public Types inherited from CDiscrepancySet
enum	EOutput { eOutput_Summary = 1 << 0 , eOutput_Fatal = 1 << 1 , eOutput_Ext = 1 << 2 , eOutput_Files = 1 << 3 }
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CDiscrepancyContext (objects::CScope &scope)
CRef< CDiscrepancyProduct >	RunTests (const TTestNamesSet &testnames, const CSerialObject &object, const string &filename) override
CRef< CDiscrepancyProduct >	GetProduct () override
void	AddTest (eTestNames name) override
void	AddTest (string_view name) override
void	Push (const CSerialObject &root, const string &fname) override
void	Parse () override
void	Parse (const CSerialObject &root, const string &fname)
void	ParseObject (const CBioseq &root)
void	ParseObject (const CBioseq_set &root)
void	ParseObject (const CSeq_entry &root)
void	ParseObject (const CSeq_submit &root)
void	ParseStream (CObjectIStream &stream, const string &fname, bool skip, const string &default_header=kEmptyStr) override
void	ParseStrings (const string &fname) override
unsigned	Summarize () override
map< string, size_t >	Autofix () override
void	Autofix (TReportObjectList &tofix, map< string, size_t > &rep, const string &default_header=kEmptyStr) override
void	AutofixFile (vector< CDiscrepancyObject * > &fixes, const string &default_header)
TDiscrepancyCaseMap	GetTests () const override
CParseNode *	FindNode (const CRefNode &obj)
const CObject *	GetMore (CReportObj &obj)
const CSerialObject *	FindObject (CReportObj &obj, bool alt=false) override
void	ReplaceObject (CReportObj &obj, CSerialObject *, bool alt=false)
void	ReplaceSeq_feat (CReportObj &obj, const CSeq_feat &old_feat, CSeq_feat &new_feat, bool alt=false)
CBioseq_set_Handle	GetBioseq_setHandle (const CBioseq_set &bss)
CBioseq_EditHandle	GetBioseqHandle (const CBioseq &bs)
const string &	CurrentText () const
const CBioseq &	CurrentBioseq () const
const CBioseq_set &	CurrentBioseq_set () const
const CSeqSummary &	CurrentBioseqSummary () const
unsigned char	ReadFlags () const
void	PropagateFlags (unsigned char f)
objects::CScope &	GetScope () const
void	SetSuspectRules (const string &name, bool read=true) override
CConstRef< CSuspect_rule_set >	GetProductRules ()
CConstRef< CSuspect_rule_set >	GetOrganelleProductRules ()
bool	HasLineage (const CBioSource *biosrc, const string &lineage) const
bool	IsEukaryotic (const CBioSource *biosrc) const
bool	IsBacterial (const CBioSource *biosrc) const
bool	IsViral (const CBioSource *biosrc) const
const CSeqSummary &	GetSeqSummary ()
void	BuildSeqSummary (const CBioseq &bs, CSeqSummary &summary)
bool	InGenProdSet () const
CConstRef< CSeqdesc >	GetTitle () const
CConstRef< CSeqdesc >	GetMolinfo () const
CConstRef< CSeqdesc >	GetBiosource () const
const vector< CConstRef< CSeqdesc > > &	GetSetBiosources () const
bool	IsBadLocusTagFormat (const string &locus_tag) const
bool	IsRefseq () const
bool	IsBGPipe ()
bool	IsPseudo (const CSeq_feat &feat)
const CSeq_feat *	GetGeneForFeature (const CSeq_feat &feat)
string	GetProdForFeature (const CSeq_feat &feat)
void	CollectFeature (const CSeq_feat &feat)
void	ClearFeatureList ()
const vector< const CSeq_feat * > &	FeatAll ()
const vector< const CSeq_feat * > &	FeatGenes ()
const vector< const CSeq_feat * > &	FeatPseudo ()
const vector< const CSeq_feat * > &	FeatCDS ()
const vector< const CSeq_feat * > &	FeatMRNAs ()
const vector< const CSeq_feat * > &	FeatRRNAs ()
const vector< const CSeq_feat * > &	FeatTRNAs ()
const vector< const CSeq_feat * > &	Feat_RNAs ()
const vector< const CSeq_feat * > &	FeatExons ()
const vector< const CSeq_feat * > &	FeatIntrons ()
const vector< const CSeq_feat * > &	FeatMisc ()
sequence::ECompare	Compare (const CSeq_loc &loc1, const CSeq_loc &loc2) const
CRefNode *	ContainingSet (CRefNode &ref)
CRef< CDiscrepancyObject >	BioseqObjRef (EFixType fix=eFixNone, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	BioseqSetObjRef (bool fix=false, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	SubmitBlockObjRef (bool fix=false, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	SeqFeatObjRef (const CSeq_feat &feat, EFixType fix=eFixNone, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	SeqFeatObjRef (const CSeq_feat &feat, const CObject *fix, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	SeqdescObjRef (const CSeqdesc &desc, const CObject *fix=nullptr, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	BiosourceObjRef (const CBioSource &biosrc, bool fix=false, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	PubdescObjRef (const CPubdesc &pubdesc, bool fix=false, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	AuthorsObjRef (const CAuth_list &authors, bool fix=false, const CObject *more=nullptr)
CRef< CDiscrepancyObject >	StringObjRef (const CObject *fix=nullptr, const CObject *more=nullptr)
bool	IsBioseq () const
const CPub *	AuthPub (const CAuth_list *a) const
CSeqdesc_vec	GetSeqdesc ()
CSeq_feat_vec	GetFeat ()
CSeqdesc_run	GetAllSeqdesc ()
CSeq_feat_run	GetAllFeat ()
const vector< const CBioSource * > &	GetBiosources () const
const vector< const CPubdesc * > &	GetPubdescs () const
const vector< const CAuth_list * > &	GetAuthors () const
const CPerson_id *	GetPerson_id () const
const CSubmit_block *	GetSubmit_block () const
Public Member Functions inherited from CDiscrepancySet
virtual	~CDiscrepancySet ()
void	SetUserData (void *p)
void *	GetUserData () const
const string &	GetLineage () const
void	SetLineage (const string &s)
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Static Public Member Functions
static bool	IsUnculturedNonOrganelleName (const string &taxname)
static bool	HasLineage (const CBioSource &biosrc, const string &def_lineage, const string &type)
static bool	IsOrganelle (const CBioSource *biosrc)
static string	GetGenomeName (unsigned n)
static string	GetAminoacidName (const CSeq_feat &feat)
Static Public Member Functions inherited from CDiscrepancySet
static void	SetGui (bool b)
static bool	IsGui ()
static CRef< CDiscrepancySet >	New (objects::CScope &scope)
static string	Format (const string &str, unsigned int count)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Protected Types
enum	EObjType {   eNone , eFile , eSubmit , eSeqSet ,   eSeqSet_NucProt , eSeqSet_GenProd , eSeqSet_SegSet , eSeqSet_Genome ,   eSeqSet_Funny , eBioseq , eSeqFeat , eSeqDesc ,   eSubmitBlock , eString }

Protected Member Functions
CParseNode *	FindLocalNode (const CParseNode &node, const CSeq_feat &feat) const
CParseNode *	FindNode (const CObject *obj) const
CParseNode *	FindNode (const CSeq_feat &feat) const
CParseNode *	FindNode (const CSeqdesc &desc) const
bool	CanFix ()
bool	CanFixBioseq_set ()
bool	CanFixBioseq ()
bool	CanFixSeq_annot ()
bool	CanFixSeqdesc ()
bool	CanFixSubmit_block ()
bool	CanFixBioseq (CRefNode &refnode)
bool	CanFixBioseq_set (CRefNode &refnode)
bool	CanFixFeat (CRefNode &refnode)
bool	CanFixDesc (CRefNode &refnode)
bool	CanFixSubmit_block (CRefNode &refnode)
void	AutofixBioseq ()
void	AutofixBioseq_set ()
void	AutofixSeq_annot ()
void	AutofixSeq_descr ()
void	AutofixSubmit_block ()
bool	Skip ()
void	Extend (CParseNode &node, CObjectIStream &stream)
void	ParseAll (CParseNode &node)
void	Populate (CParseNode &node)
void	PopulateBioseq (CParseNode &node)
void	PopulateSeqSet (CParseNode &node)
void	PopulateSubmit (CParseNode &node)
void	RunTests ()
void	PushNode (EObjType)
void	PopNode ()
bool	IsPseudo (const CParseNode &node)
const CParseNode *	GeneForFeature (const CParseNode &node)
string	ProdForFeature (const CParseNode &node)
Protected Member Functions inherited from CDiscrepancySet
	CDiscrepancySet ()
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Static Protected Member Functions
static bool	InNucProtSet (const CParseNode *node)
static bool	InGenProdSet (const CParseNode *node)
static bool	IsSeqSet (EObjType n)
static string	TypeName (EObjType n)
static bool	CompareRefs (CRef< CReportObj > a, CRef< CReportObj > b)

Protected Attributes
CRef< objects::CScope >	m_Scope
CRef< feature::CFeatTree >	m_FeatTree
TDiscrepancyCoreMap	m_Tests
vector< CConstRef< CBioseq_set > >	m_Bioseq_set_Stack
CBioseq_Handle	m_Current_Bioseq_Handle
CConstRef< CBioseq >	m_Current_Bioseq
CConstRef< CSubmit_block >	m_Current_Submit_block
CRef< CSimpleTypeObject< string > >	m_Current_Submit_block_StringObj
CRef< CSimpleTypeObject< string > >	m_Current_Cit_sub_StringObj
CConstRef< CSeqdesc >	m_Current_Seqdesc
CConstRef< CSeq_feat >	m_Current_Seq_feat
CConstRef< CPub >	m_Current_Pub
CConstRef< CPub_equiv >	m_Current_Pub_equiv
CConstRef< CSuspect_rule_set >	m_ProductRules
CConstRef< CSuspect_rule_set >	m_OrganelleProductRules
string	m_SuspectRules
vector< const CSeq_feat * >	m_FeatAll
vector< const CSeq_feat * >	m_FeatGenes
vector< const CSeq_feat * >	m_FeatPseudo
vector< const CSeq_feat * >	m_FeatCDS
vector< const CSeq_feat * >	m_FeatMRNAs
vector< const CSeq_feat * >	m_FeatRRNAs
vector< const CSeq_feat * >	m_FeatTRNAs
vector< const CSeq_feat * >	m_Feat_RNAs
vector< const CSeq_feat * >	m_FeatExons
vector< const CSeq_feat * >	m_FeatIntrons
vector< const CSeq_feat * >	m_FeatMisc
map< const CRefNode *, CParseNode * >	m_NodeMap
vector< CDiscrepancyObject * > *	m_Fixes
CRef< CBioseq_set >	m_AF_Bioseq_set
CRef< CBioseq >	m_AF_Bioseq
CRef< CSeq_annot >	m_AF_Seq_annot
CRef< CSeq_descr >	m_AF_Seq_descr
CRef< CSubmit_block >	m_AF_Submit_block
ct::const_bitset< static_cast< size_t >eTestTypes::max_num_types), eTestTypes >	m_Enabled
vector< CDiscrepancyCore * >	m_All_SEQUENCE
vector< CDiscrepancyCore * >	m_All_SEQ_SET
vector< CDiscrepancyCore * >	m_All_FEAT
vector< CDiscrepancyCore * >	m_All_DESC
vector< CDiscrepancyCore * >	m_All_BIOSRC
vector< CDiscrepancyCore * >	m_All_PUBDESC
vector< CDiscrepancyCore * >	m_All_AUTHORS
vector< CDiscrepancyCore * >	m_All_SUBMIT
vector< CDiscrepancyCore * >	m_All_STRING
bool	m_Skip
CRef< CParseNode >	m_RootNode
CRef< CParseNode >	m_CurrentNode
Protected Attributes inherited from CDiscrepancySet
string	m_Lineage
void *	m_UserData = nullptr

Friends
class	CReadHook_Bioseq_set
	BIG FILE. More...
class	CReadHook_Bioseq_set_class
class	CReadHook_Bioseq
class	CCopyHook_Bioseq_set
class	CCopyHook_Bioseq
class	CCopyHook_Seq_descr
class	CCopyHook_Seq_annot
class	CCopyHook_Submit_block
class	CDiscrepancyObject

Additional Inherited Members
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...
Static Protected Attributes inherited from CDiscrepancySet
static std::atomic< bool >	m_Gui = false

Detailed Description

Definition at line 322 of file discrepancy_core.hpp.

Member Enumeration Documentation

EFixType

enum CDiscrepancyContext::EFixType

BIG FILE.

Enumerator
eFixNone
eFixSelf
eFixParent
eFixSet

Definition at line 423 of file discrepancy_core.hpp.

EFlag

enum CDiscrepancyContext::EFlag

Enumerator
eHasRearranged
eHasSatFeat
eHasNonSatFeat

Definition at line 329 of file discrepancy_core.hpp.

EObjType

enum CDiscrepancyContext::EObjType

protected

Enumerator
eNone
eFile
eSubmit
eSeqSet
eSeqSet_NucProt
eSeqSet_GenProd
eSeqSet_SegSet
eSeqSet_Genome
eSeqSet_Funny
eBioseq
eSeqFeat
eSeqDesc
eSubmitBlock
eString

Definition at line 634 of file discrepancy_core.hpp.

Constructor & Destructor Documentation

CDiscrepancyContext()

CDiscrepancyContext::CDiscrepancyContext ( objects::CScope &  scope )

inline

Definition at line 335 of file discrepancy_core.hpp.

Member Function Documentation

AddTest() [1/2]

void CDiscrepancyContext::AddTest ( eTestNames  name )

overridevirtual

Implements CDiscrepancySet.

Definition at line 527 of file discrepancy_core.cpp.

References AUTHORS, BIOSRC, CDiscrepancyCaseProps::Constructor, DESC, Empty(), FEAT, CCaseRegistry::GetProps(), m_Enabled, m_Tests, PUBDESC, REGISTER_DISCREPANCY_TYPE, SEQ_SET, SEQUENCE, STRING, SUBMIT, and test.

Referenced by AddTest(), and RunTests().

AddTest() [2/2]

void CDiscrepancyContext::AddTest ( string_view  name )

overridevirtual

Implements CDiscrepancySet.

Definition at line 522 of file discrepancy_core.cpp.

References AddTest(), and GetDiscrepancyCaseName().

AuthorsObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::AuthorsObjRef	(	const CAuth_list &	authors,
		bool	fix = false,
		const CObject *	more = nullptr
	)

Definition at line 935 of file discrepancy_context.cpp.

References _ASSERT, CDiscrepancyObject, eSeqDesc, eSeqFeat, CDiscrepancyObject::GetTextObjectDescription(), m_CurrentNode, m_Scope, and CRef< C, Locker >::Reset().

AuthPub()

const CPub* CDiscrepancyContext::AuthPub ( const CAuth_list *  a ) const

inline

Definition at line 442 of file discrepancy_core.hpp.

References a, m_CurrentNode, and nullptr.

Autofix() [1/2]

map< string, size_t > CDiscrepancyContext::Autofix ( )

overridevirtual

Implements CDiscrepancySet.

Definition at line 894 of file discrepancy_core.cpp.

References m_Tests.

Referenced by AutofixBioseq(), AutofixBioseq_set(), AutofixSeq_annot(), AutofixSeq_descr(), and AutofixSubmit_block().

Autofix() [2/2]

void CDiscrepancyContext::Autofix ( TReportObjectList &  tofix, map< string, size_t > &  rep, const string &  default_header = kEmptyStr  )

overridevirtual

Implements CDiscrepancySet.

Definition at line 722 of file discrepancy_stream.cpp.

References CDiscrepancyCore::Autofix(), AutofixFile(), CompareRefs(), eFile, CDiscrepancyObject::m_Case, CDiscrepancyObject::m_Fix, CDiscrepancyContext::CRefNode::m_Parent, result, and ct::sort().

AutofixBioseq()

void CDiscrepancyContext::AutofixBioseq ( )

protected

Definition at line 1089 of file discrepancy_stream.cpp.

References Autofix(), CanFixBioseq(), CSeq_descr_Base::CanGet(), CBioseq_Base::CanGetDescr(), CSeq_descr_Base::Get(), CBioseq_Base::GetAnnot(), CBioseq_Base::GetDescr(), CBioseq_Base::IsSetAnnot(), m_CurrentNode, m_Fixes, m_NodeMap, and result.

Referenced by AutofixBioseq_set(), and CCopyHook_Bioseq::CopyObject().

AutofixBioseq_set()

void CDiscrepancyContext::AutofixBioseq_set ( )

protected

Definition at line 1048 of file discrepancy_stream.cpp.

References Autofix(), AutofixBioseq(), CanFixBioseq_set(), CSeq_descr_Base::CanGet(), CBioseq_set_Base::CanGetDescr(), eBioseq, eSeqSet, CSeq_descr_Base::Get(), CBioseq_set_Base::GetAnnot(), CBioseq_set_Base::GetDescr(), CBioseq_set_Base::GetSeq_set(), CBioseq_set_Base::IsSetAnnot(), m_CurrentNode, m_Fixes, m_NodeMap, PopNode(), PushNode(), and result.

Referenced by CCopyHook_Bioseq_set::CopyObject().

AutofixFile()

void CDiscrepancyContext::AutofixFile	(	vector< CDiscrepancyObject * > &	fixes,
		const string &	default_header
	)

Definition at line 766 of file discrepancy_stream.cpp.

References CCopyHook_Bioseq, CCopyHook_Bioseq_set, CCopyHook_Seq_annot, CCopyHook_Seq_descr, CCopyHook_Submit_block, CObjectStreamCopier::Copy(), eFile, eNone, eSerial_AsnText, eSubmit, eUnknown, in(), m_CurrentNode, m_Fixes, CDiscrepancyContext::CRefNode::m_Parent, m_RootNode, NCBI_THROW, CObjectOStream::Open(), OpenUncompressedStream(), out(), PopNode(), PushNode(), and CObjectTypeInfo::SetLocalCopyHook().

Referenced by Autofix().

AutofixSeq_annot()

void CDiscrepancyContext::AutofixSeq_annot ( )

protected

Definition at line 999 of file discrepancy_stream.cpp.

References Autofix(), CanFixFeat(), CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_annot::IsFtable(), m_AF_Seq_annot, m_CurrentNode, m_Fixes, m_NodeMap, and result.

Referenced by CCopyHook_Seq_annot::CopyObject().

AutofixSeq_descr()

void CDiscrepancyContext::AutofixSeq_descr ( )

protected

Definition at line 1016 of file discrepancy_stream.cpp.

References Autofix(), CanFixDesc(), CSeq_descr_Base::CanGet(), CSeq_descr_Base::Get(), m_AF_Seq_descr, m_CurrentNode, m_Fixes, m_NodeMap, and result.

Referenced by CCopyHook_Seq_descr::CopyObject().

AutofixSubmit_block()

void CDiscrepancyContext::AutofixSubmit_block ( )

protected

Definition at line 1033 of file discrepancy_stream.cpp.

References Autofix(), CanFixSubmit_block(), eSubmitBlock, CRef< C, Locker >::GetPointer(), m_AF_Submit_block, m_Fixes, m_NodeMap, CRef< C, Locker >::Reset(), and result.

Referenced by CCopyHook_Submit_block::CopyObject().

BioseqObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::BioseqObjRef	(	EFixType	fix = eFixNone,
		const CObject *	more = nullptr
	)

Definition at line 811 of file discrepancy_context.cpp.

References CDiscrepancyObject, ContainingSet(), eFixParent, eFixSelf, eFixSet, and m_CurrentNode.

BioseqSetObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::BioseqSetObjRef	(	bool	fix = false,
		const CObject *	more = nullptr
	)

Definition at line 828 of file discrepancy_context.cpp.

References CDiscrepancyObject, and m_CurrentNode.

BiosourceObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::BiosourceObjRef	(	const CBioSource &	biosrc,
		bool	fix = false,
		const CObject *	more = nullptr
	)

Definition at line 895 of file discrepancy_context.cpp.

References CDiscrepancyObject, eSeqFeat, CDiscrepancyObject::GetTextObjectDescription(), m_CurrentNode, m_Scope, and CRef< C, Locker >::Reset().

BuildSeqSummary()

void CDiscrepancyContext::BuildSeqSummary	(	const CBioseq &	bs,
		CSeqSummary &	summary
	)

Definition at line 404 of file discrepancy_context.cpp.

References _notN(), CSeq_id::BaseBestRankScore(), CSeqSummary::clear(), CountNucleotides(), CSeqMap::CreateSeqMapForBioseq(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Other, CSeq_id::eContent, CSeqSummary::EndsWithGap, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::eSeqRef, CSeqMap::fFindData, CSeqMap::fFindGap, CSeqMap::fFindLeafRef, CSeqSummary::First, CSeqSummary::Gaps, CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_id::GetLabel(), CSeq_inst_Base::GetLength(), GetScope(), CSeqSummary::HasRef, CSeq_id::kMaxScore, CSeqSummary::Label, CSeqSummary::Len, and SSeqMapSelector::SetFlags().

Referenced by PopulateBioseq().

CanFix()

bool CDiscrepancyContext::CanFix ( )

protected

CanFixBioseq() [1/2]

bool CDiscrepancyContext::CanFixBioseq ( )

protected

Definition at line 895 of file discrepancy_stream.cpp.

References m_Fixes.

Referenced by AutofixBioseq(), and CCopyHook_Bioseq::CopyObject().

CanFixBioseq() [2/2]

bool CDiscrepancyContext::CanFixBioseq ( CRefNode &  refnode )

protected

Definition at line 875 of file discrepancy_stream.cpp.

References A, B, eBioseq, m_CurrentNode, and CDiscrepancyContext::CRefNode::m_Type.

CanFixBioseq_set() [1/2]

bool CDiscrepancyContext::CanFixBioseq_set ( )

protected

Definition at line 863 of file discrepancy_stream.cpp.

References m_Fixes.

Referenced by AutofixBioseq_set(), and CCopyHook_Bioseq_set::CopyObject().

CanFixBioseq_set() [2/2]

bool CDiscrepancyContext::CanFixBioseq_set ( CRefNode &  refnode )

protected

Definition at line 843 of file discrepancy_stream.cpp.

References A, B, IsSeqSet(), m_CurrentNode, and CDiscrepancyContext::CRefNode::m_Type.

CanFixDesc()

bool CDiscrepancyContext::CanFixDesc ( CRefNode &  refnode )

protected

Definition at line 937 of file discrepancy_stream.cpp.

References A, B, eSeqDesc, m_CurrentNode, CDiscrepancyContext::CRefNode::m_Parent, and CDiscrepancyContext::CRefNode::m_Type.

Referenced by AutofixSeq_descr(), and CanFixSeqdesc().

CanFixFeat()

bool CDiscrepancyContext::CanFixFeat ( CRefNode &  refnode )

protected

Definition at line 906 of file discrepancy_stream.cpp.

References A, B, eSeqFeat, m_CurrentNode, CDiscrepancyContext::CRefNode::m_Parent, and CDiscrepancyContext::CRefNode::m_Type.

Referenced by AutofixSeq_annot(), and CanFixSeq_annot().

CanFixSeq_annot()

bool CDiscrepancyContext::CanFixSeq_annot ( )

protected

Definition at line 926 of file discrepancy_stream.cpp.

References CanFixFeat(), and m_Fixes.

Referenced by CCopyHook_Seq_annot::CopyObject().

CanFixSeqdesc()

bool CDiscrepancyContext::CanFixSeqdesc ( )

protected

Definition at line 957 of file discrepancy_stream.cpp.

References CanFixDesc(), and m_Fixes.

Referenced by CCopyHook_Seq_descr::CopyObject().

CanFixSubmit_block() [1/2]

bool CDiscrepancyContext::CanFixSubmit_block ( )

protected

Definition at line 988 of file discrepancy_stream.cpp.

References m_Fixes.

Referenced by AutofixSubmit_block(), and CCopyHook_Submit_block::CopyObject().

CanFixSubmit_block() [2/2]

bool CDiscrepancyContext::CanFixSubmit_block ( CRefNode &  refnode )

protected

Definition at line 968 of file discrepancy_stream.cpp.

References A, B, eSubmit, m_CurrentNode, and CDiscrepancyContext::CRefNode::m_Type.

ClearFeatureList()

void CDiscrepancyContext::ClearFeatureList

(

)

Definition at line 640 of file discrepancy_context.cpp.

References m_Feat_RNAs, m_FeatAll, m_FeatCDS, m_FeatExons, m_FeatGenes, m_FeatIntrons, m_FeatMisc, m_FeatMRNAs, m_FeatPseudo, m_FeatRRNAs, and m_FeatTRNAs.

Referenced by RunTests().

CollectFeature()

void CDiscrepancyContext::CollectFeature

(

const CSeq_feat &

feat

)

Definition at line 656 of file discrepancy_context.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_tRNA, CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), IsPseudo(), CSeqFeatData_Base::IsRna(), m_Feat_RNAs, m_FeatAll, m_FeatCDS, m_FeatExons, m_FeatGenes, m_FeatIntrons, m_FeatMisc, m_FeatMRNAs, m_FeatPseudo, m_FeatRRNAs, and m_FeatTRNAs.

Referenced by RunTests().

Compare()

sequence::ECompare CDiscrepancyContext::Compare	(	const CSeq_loc &	loc1,
		const CSeq_loc &	loc2
	)		const

Definition at line 696 of file discrepancy_context.cpp.

References Compare(), eNoOverlap, fCompareOverlapping, GetScope(), CSeq_loc::GetTotalRange(), r1, and r2.

CompareRefs()

bool CDiscrepancyContext::CompareRefs ( CRef< CReportObj >  a, CRef< CReportObj >  b  )

staticprotected

Definition at line 854 of file discrepancy_core.cpp.

References a, A, b, B, eSeqDesc, eSeqFeat, i, CDiscrepancyContext::CRefNode::m_Parent, CDiscrepancyObject::m_Ref, min(), and n.

Referenced by Autofix().

ContainingSet()

CDiscrepancyContext::CRefNode * CDiscrepancyContext::ContainingSet

(

CDiscrepancyContext::CRefNode &

ref

)

Definition at line 796 of file discrepancy_context.cpp.

References eSeqSet_GenProd, eSeqSet_NucProt, IsSeqSet(), CDiscrepancyContext::CRefNode::m_Parent, and r().

Referenced by BioseqObjRef(), and SeqFeatObjRef().

CurrentBioseq()

const CBioseq& CDiscrepancyContext::CurrentBioseq ( ) const

inline

Definition at line 369 of file discrepancy_core.hpp.

References m_CurrentNode.

Referenced by IsRefseq().

CurrentBioseq_set()

const CBioseq_set& CDiscrepancyContext::CurrentBioseq_set ( ) const

inline

Definition at line 370 of file discrepancy_core.hpp.

References m_CurrentNode.

CurrentBioseqSummary()

const CSeqSummary & CDiscrepancyContext::CurrentBioseqSummary

(

)

const

Definition at line 58 of file discrepancy_context.cpp.

CurrentText()

const string& CDiscrepancyContext::CurrentText ( ) const

inline

Definition at line 368 of file discrepancy_core.hpp.

References m_CurrentNode.

Extend()

void CDiscrepancyContext::Extend ( CParseNode &  node, CObjectIStream &  stream  )

protected

Definition at line 249 of file discrepancy_stream.cpp.

References eBioseq, CObjectIStream::eNoFileHeader, eSeqSet, eSeqSet_GenProd, eSeqSet_NucProt, i, InGenProdSet(), InNucProtSet(), CDiscrepancyContext::CParseNode::m_Children, m_CurrentNode, m_FeatTree, CDiscrepancyContext::CParseNode::m_Obj, CDiscrepancyContext::CParseNode::m_Pos, CDiscrepancyContext::CParseNode::m_Repeat, m_Scope, CDiscrepancyContext::CParseNode::m_Type, ObjectInfo(), Populate(), CObjectIStream::Read(), CRef< C, Locker >::Reset(), RunTests(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), and CObjectIStream::SetStreamPos().

Referenced by ParseStream().

Feat_RNAs()

const vector<const CSeq_feat*>& CDiscrepancyContext::Feat_RNAs ( )

inline

Definition at line 415 of file discrepancy_core.hpp.

References m_Feat_RNAs.

FeatAll()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatAll ( )

inline

Definition at line 408 of file discrepancy_core.hpp.

References m_FeatAll.

FeatCDS()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatCDS ( )

inline

Definition at line 411 of file discrepancy_core.hpp.

References m_FeatCDS.

FeatExons()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatExons ( )

inline

Definition at line 416 of file discrepancy_core.hpp.

References m_FeatExons.

FeatGenes()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatGenes ( )

inline

Definition at line 409 of file discrepancy_core.hpp.

References m_FeatGenes.

FeatIntrons()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatIntrons ( )

inline

Definition at line 417 of file discrepancy_core.hpp.

References m_FeatIntrons.

FeatMisc()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatMisc ( )

inline

Definition at line 418 of file discrepancy_core.hpp.

References m_FeatMisc.

FeatMRNAs()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatMRNAs ( )

inline

Definition at line 412 of file discrepancy_core.hpp.

References m_FeatMRNAs.

FeatPseudo()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatPseudo ( )

inline

Definition at line 410 of file discrepancy_core.hpp.

References m_FeatPseudo.

FeatRRNAs()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatRRNAs ( )

inline

Definition at line 413 of file discrepancy_core.hpp.

References m_FeatRRNAs.

FeatTRNAs()

const vector<const CSeq_feat*>& CDiscrepancyContext::FeatTRNAs ( )

inline

Definition at line 414 of file discrepancy_core.hpp.

References m_FeatTRNAs.

FindLocalNode()

CDiscrepancyContext::CParseNode * CDiscrepancyContext::FindLocalNode ( const CParseNode &  node, const CSeq_feat &  feat  ) const

protected

Definition at line 757 of file discrepancy_context.cpp.

References CDiscrepancyContext::CParseNode::m_FeatureMap, and nullptr.

Referenced by FindNode().

FindNode() [1/4]

CDiscrepancyContext::CParseNode * CDiscrepancyContext::FindNode ( const CObject *  obj ) const

protected

Definition at line 736 of file discrepancy_context.cpp.

References FindNode(), and m_CurrentNode.

FindNode() [2/4]

CDiscrepancyContext::CParseNode * CDiscrepancyContext::FindNode

(

const CRefNode &

obj

)

Definition at line 501 of file discrepancy_stream.cpp.

References eSeqDesc, eSeqFeat, CDiscrepancyContext::CParseNode::m_Children, CDiscrepancyContext::CParseNode::m_Descriptors, CDiscrepancyContext::CParseNode::m_Features, CDiscrepancyContext::CRefNode::m_Index, m_NodeMap, CDiscrepancyContext::CRefNode::m_Parent, and CDiscrepancyContext::CRefNode::m_Type.

Referenced by FindNode(), FindObject(), GeneForFeature(), GetGeneForFeature(), GetProdForFeature(), IsPseudo(), ReplaceObject(), SeqdescObjRef(), SeqFeatObjRef(), and StringObjRef().

FindNode() [3/4]

CDiscrepancyContext::CParseNode * CDiscrepancyContext::FindNode ( const CSeq_feat &  feat ) const

protected

Definition at line 764 of file discrepancy_context.cpp.

References eSeqSet_GenProd, eSeqSet_NucProt, FindLocalNode(), m_CurrentNode, and CDiscrepancyContext::CParseNode::m_FeatureMap.

FindNode() [4/4]

CDiscrepancyContext::CParseNode * CDiscrepancyContext::FindNode ( const CSeqdesc &  desc ) const

protected

Definition at line 784 of file discrepancy_context.cpp.

References m_CurrentNode, and CDiscrepancyContext::CParseNode::m_DescriptorMap.

FindObject()

const CSerialObject * CDiscrepancyContext::FindObject ( CReportObj &  obj, bool  alt = false  )

overridevirtual

Implements CDiscrepancySet.

Definition at line 528 of file discrepancy_stream.cpp.

References FindNode(), CConstRef< C, Locker >::GetPointerOrNull(), CDiscrepancyObject::m_Fix, CDiscrepancyContext::CParseNode::m_Obj, and CDiscrepancyObject::m_Ref.

GeneForFeature()

const CDiscrepancyContext::CParseNode * CDiscrepancyContext::GeneForFeature ( const CParseNode &  node )

protected

Definition at line 565 of file discrepancy_context.cpp.

References CDiscrepancyContext::CParseNode::eKnownGene, FindNode(), GetGeneForFeature(), CDiscrepancyContext::CParseNode::m_Gene, CDiscrepancyContext::CParseNode::m_Info, CDiscrepancyContext::CParseNode::m_Obj, and m_Scope.

Referenced by GetGeneForFeature(), and IsPseudo().

GetAllFeat()

CSeq_feat_run CDiscrepancyContext::GetAllFeat ( )

inline

Definition at line 544 of file discrepancy_core.hpp.

References m_CurrentNode.

Referenced by RunTests().

GetAllSeqdesc()

CSeqdesc_run CDiscrepancyContext::GetAllSeqdesc ( )

inline

Definition at line 543 of file discrepancy_core.hpp.

References m_CurrentNode.

Referenced by IsBGPipe().

GetAminoacidName()

string CDiscrepancyContext::GetAminoacidName ( const CSeq_feat &  feat )

static

Definition at line 473 of file discrepancy_context.cpp.

References fFGL_Content, GetLabel(), and n.

GetAuthors()

const vector<const CAuth_list*>& CDiscrepancyContext::GetAuthors ( void  ) const

inline

Definition at line 547 of file discrepancy_core.hpp.

References m_CurrentNode.

GetBioseq_setHandle()

CBioseq_set_Handle CDiscrepancyContext::GetBioseq_setHandle ( const CBioseq_set &  bss )

inline

Definition at line 365 of file discrepancy_core.hpp.

References m_Scope.

GetBioseqHandle()

CBioseq_EditHandle CDiscrepancyContext::GetBioseqHandle ( const CBioseq &  bs )

inline

Definition at line 366 of file discrepancy_core.hpp.

References m_Scope.

GetBiosource()

CConstRef<CSeqdesc> CDiscrepancyContext::GetBiosource ( ) const

inline

Definition at line 395 of file discrepancy_core.hpp.

References m_CurrentNode.

GetBiosources()

const vector<const CBioSource*>& CDiscrepancyContext::GetBiosources ( ) const

inline

Definition at line 545 of file discrepancy_core.hpp.

References m_CurrentNode.

GetFeat()

CSeq_feat_vec CDiscrepancyContext::GetFeat ( void  )

inline

Definition at line 542 of file discrepancy_core.hpp.

References m_CurrentNode.

GetGeneForFeature()

const CSeq_feat * CDiscrepancyContext::GetGeneForFeature

(

const CSeq_feat &

feat

)

Definition at line 552 of file discrepancy_context.cpp.

References FindNode(), and GeneForFeature().

GetGenomeName()

string CDiscrepancyContext::GetGenomeName ( unsigned  n )

static

Definition at line 459 of file discrepancy_context.cpp.

References ENUM_METHOD_NAME, eSource_location_chromatophore, eSource_location_unknown, G, i, kEmptyStr, n, and str().

GetMolinfo()

CConstRef<CSeqdesc> CDiscrepancyContext::GetMolinfo ( void  ) const

inline

Definition at line 394 of file discrepancy_core.hpp.

References m_CurrentNode.

GetMore()

const CObject * CDiscrepancyContext::GetMore ( CReportObj &  obj )

inline

Definition at line 923 of file discrepancy_core.hpp.

GetOrganelleProductRules()

CConstRef< CSuspect_rule_set > CDiscrepancyContext::GetOrganelleProductRules

(

)

Definition at line 84 of file discrepancy_context.cpp.

References GetOrganelleProductRules(), and m_OrganelleProductRules.

GetPerson_id()

const CPerson_id * CDiscrepancyContext::GetPerson_id

(

)

const

Definition at line 710 of file discrepancy_context.cpp.

References eSubmit, CContact_info_Base::GetContact(), CSubmit_block_Base::GetContact(), CAuthor_Base::GetName(), CSeq_submit_Base::GetSub(), CContact_info_Base::IsSetContact(), CSubmit_block_Base::IsSetContact(), CAuthor_Base::IsSetName(), CSeq_submit_Base::IsSetSub(), and m_CurrentNode.

GetProdForFeature()

string CDiscrepancyContext::GetProdForFeature

(

const CSeq_feat &

feat

)

Definition at line 559 of file discrepancy_context.cpp.

References FindNode(), and ProdForFeature().

GetProduct()

CRef< CDiscrepancyProduct > CDiscrepancyContext::GetProduct ( void  )

overridevirtual

Implements CDiscrepancySet.

Definition at line 973 of file discrepancy_context.cpp.

References m_Tests, and Ref().

Referenced by RunTests().

GetProductRules()

CConstRef< CSuspect_rule_set > CDiscrepancyContext::GetProductRules

(

)

Definition at line 75 of file discrepancy_context.cpp.

References GetProductRules(), m_ProductRules, and m_SuspectRules.

GetPubdescs()

const vector<const CPubdesc*>& CDiscrepancyContext::GetPubdescs ( ) const

inline

Definition at line 546 of file discrepancy_core.hpp.

References m_CurrentNode.

GetScope()

objects::CScope& CDiscrepancyContext::GetScope ( void  ) const

inline

Definition at line 375 of file discrepancy_core.hpp.

Referenced by BuildSeqSummary(), Compare(), and ReplaceSeq_feat().

GetSeqdesc()

CSeqdesc_vec CDiscrepancyContext::GetSeqdesc ( )

inline

Definition at line 541 of file discrepancy_core.hpp.

References m_CurrentNode.

GetSeqSummary()

const CSeqSummary& CDiscrepancyContext::GetSeqSummary ( )

inline

Definition at line 390 of file discrepancy_core.hpp.

References m_CurrentNode.

GetSetBiosources()

const vector<CConstRef<CSeqdesc> >& CDiscrepancyContext::GetSetBiosources ( ) const

inline

Definition at line 396 of file discrepancy_core.hpp.

References m_CurrentNode.

GetSubmit_block()

const CSubmit_block * CDiscrepancyContext::GetSubmit_block

(

)

const

Definition at line 722 of file discrepancy_context.cpp.

References eSubmit, CSeq_submit_Base::GetSub(), CSeq_submit_Base::IsSetSub(), and m_CurrentNode.

GetTests()

TDiscrepancyCaseMap CDiscrepancyContext::GetTests ( ) const

overridevirtual

Implements CDiscrepancySet.

Definition at line 912 of file discrepancy_core.cpp.

References m_Tests.

GetTitle()

CConstRef<CSeqdesc> CDiscrepancyContext::GetTitle ( void  ) const

inline

Definition at line 393 of file discrepancy_core.hpp.

References m_CurrentNode.

HasLineage() [1/2]

bool CDiscrepancyContext::HasLineage ( const CBioSource &  biosrc, const string &  def_lineage, const string &  type  )

static

Definition at line 107 of file discrepancy_context.cpp.

References NStr::FindNoCase(), CBioSource::GetLineage(), CBioSource::IsSetLineage(), and NPOS.

Referenced by AddExceptionsToShortIntron(), HasLineage(), IsBacterial(), IsEukaryotic(), and IsViral().

HasLineage() [2/2]

bool CDiscrepancyContext::HasLineage	(	const CBioSource *	biosrc,
		const string &	lineage
	)		const

Definition at line 113 of file discrepancy_context.cpp.

References CDiscrepancySet::GetLineage(), and HasLineage().

InGenProdSet() [1/2]

bool CDiscrepancyContext::InGenProdSet ( ) const

inline

Definition at line 392 of file discrepancy_core.hpp.

References m_CurrentNode.

Referenced by Extend().

InGenProdSet() [2/2]

static bool CDiscrepancyContext::InGenProdSet ( const CParseNode *  node )

inlinestaticprotected

Definition at line 587 of file discrepancy_core.hpp.

References eSeqSet_GenProd, CDiscrepancyContext::CParseNode::m_Parent, and CDiscrepancyContext::CParseNode::m_Type.

InNucProtSet()

static bool CDiscrepancyContext::InNucProtSet ( const CParseNode *  node )

inlinestaticprotected

Definition at line 586 of file discrepancy_core.hpp.

References eSeqSet_NucProt, CDiscrepancyContext::CParseNode::m_Parent, and CDiscrepancyContext::CParseNode::m_Type.

Referenced by Extend().

IsBacterial()

bool CDiscrepancyContext::IsBacterial

(

const CBioSource *

biosrc

)

const

Definition at line 153 of file discrepancy_context.cpp.

References HasLineage().

IsBadLocusTagFormat()

bool CDiscrepancyContext::IsBadLocusTagFormat

(

const string &

locus_tag

)

const

Definition at line 485 of file discrepancy_context.cpp.

References CRegexp::IsMatch().

IsBGPipe()

bool CDiscrepancyContext::IsBGPipe

(

)

Definition at line 511 of file discrepancy_context.cpp.

References CSeqdesc_Base::e_User, NStr::eNocase, NStr::EqualNocase(), FIELD_IS_SET_AND_IS, GetAllSeqdesc(), CUser_field_Base::GetData(), CUser_object::GetFieldRef(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), m_Scope, and Type.

IsBioseq()

bool CDiscrepancyContext::IsBioseq ( void  ) const

inline

Definition at line 441 of file discrepancy_core.hpp.

References eBioseq, and m_CurrentNode.

IsEukaryotic()

bool CDiscrepancyContext::IsEukaryotic

(

const CBioSource *

biosrc

)

const

Definition at line 139 of file discrepancy_context.cpp.

References CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_plastid, CBioSource_Base::GetGenome(), CDiscrepancySet::GetLineage(), and HasLineage().

IsOrganelle()

bool CDiscrepancyContext::IsOrganelle ( const CBioSource *  biosrc )

static

Definition at line 119 of file discrepancy_context.cpp.

References CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromatophore, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_hydrogenosome, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_nucleomorph, CBioSource_Base::eGenome_plastid, CBioSource_Base::eGenome_proplastid, CBioSource_Base::GetGenome(), and CBioSource_Base::IsSetGenome().

IsPseudo() [1/2]

bool CDiscrepancyContext::IsPseudo ( const CParseNode &  node )

protected

Definition at line 596 of file discrepancy_context.cpp.

References CDiscrepancyContext::CParseNode::eIsPseudo, CDiscrepancyContext::CParseNode::eKnownPseudo, NStr::EqualNocase(), GeneForFeature(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CGene_ref_Base::GetPseudo(), CSeq_feat_Base::GetPseudo(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::GetXref(), CSeqFeatData_Base::IsGene(), IsPseudo(), CGene_ref_Base::IsSetPseudo(), CSeq_feat_Base::IsSetPseudo(), CSeq_feat_Base::IsSetQual(), CSeq_feat_Base::IsSetXref(), CDiscrepancyContext::CParseNode::m_Info, and CDiscrepancyContext::CParseNode::m_Obj.

IsPseudo() [2/2]

bool CDiscrepancyContext::IsPseudo

(

const CSeq_feat &

feat

)

Definition at line 590 of file discrepancy_context.cpp.

References FindNode().

Referenced by CollectFeature(), and IsPseudo().

IsRefseq()

bool CDiscrepancyContext::IsRefseq

(

void

)

const

Definition at line 497 of file discrepancy_context.cpp.

References CurrentBioseq(), CBioseq_Base::GetId(), and CBioseq_Base::IsSetId().

IsSeqSet()

static bool CDiscrepancyContext::IsSeqSet ( EObjType  n )

inlinestaticprotected

Definition at line 651 of file discrepancy_core.hpp.

References eSeqSet, eSeqSet_Funny, eSeqSet_Genome, eSeqSet_GenProd, eSeqSet_NucProt, eSeqSet_SegSet, and n.

Referenced by CanFixBioseq_set(), ContainingSet(), CDiscrepancyContext::CRefNode::GetBioseqLabel(), CDiscrepancyContext::CRefNode::GetText(), PopulateBioseq(), PopulateSeqSet(), and RunTests().

IsUnculturedNonOrganelleName()

bool CDiscrepancyContext::IsUnculturedNonOrganelleName ( const string &  taxname )

static

Definition at line 93 of file discrepancy_context.cpp.

References NStr::Equal().

IsViral()

bool CDiscrepancyContext::IsViral

(

const CBioSource *

biosrc

)

const

Definition at line 159 of file discrepancy_context.cpp.

References HasLineage().

Parse() [1/2]

void CDiscrepancyContext::Parse ( )

inlineoverridevirtual

Implements CDiscrepancySet.

Definition at line 343 of file discrepancy_core.hpp.

References m_RootNode, and ParseAll().

Referenced by RunTests().

Parse() [2/2]

void CDiscrepancyContext::Parse	(	const CSerialObject &	root,
		const string &	fname
	)

Definition at line 980 of file discrepancy_context.cpp.

References m_RootNode, ParseAll(), and Push().

ParseAll()

void CDiscrepancyContext::ParseAll ( CParseNode &  node )

protected

Definition at line 371 of file discrepancy_stream.cpp.

References CDiscrepancyContext::CParseNode::m_Children, m_CurrentNode, Populate(), and RunTests().

Referenced by Parse().

ParseObject() [1/4]

void CDiscrepancyContext::ParseObject

(

const CBioseq &

root

)

Definition at line 298 of file discrepancy_stream.cpp.

References eBioseq, m_CurrentNode, and PushNode().

Referenced by ParseObject(), and Push().

ParseObject() [2/4]

void CDiscrepancyContext::ParseObject

(

const CBioseq_set &

root

)

Definition at line 307 of file discrepancy_stream.cpp.

References CBioseq_set_Base::CanGetSeq_set(), CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_mut_set, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::eClass_phy_set, CBioseq_set_Base::eClass_pop_set, CBioseq_set_Base::eClass_segset, CBioseq_set_Base::eClass_small_genome_set, eSeqSet, eSeqSet_Funny, eSeqSet_Genome, eSeqSet_GenProd, eSeqSet_NucProt, eSeqSet_SegSet, CBioseq_set_Base::GetClass(), CBioseq_set_Base::GetSeq_set(), CBioseq_set_Base::IsSetClass(), m_CurrentNode, ParseObject(), and PushNode().

ParseObject() [3/4]

void CDiscrepancyContext::ParseObject

(

const CSeq_entry &

root

)

Definition at line 346 of file discrepancy_stream.cpp.

References CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), and ParseObject().

ParseObject() [4/4]

void CDiscrepancyContext::ParseObject

(

const CSeq_submit &

root

)

Definition at line 357 of file discrepancy_stream.cpp.

References CSeq_submit_Base::CanGetData(), eSubmit, CSeq_submit_Base::GetData(), CSeq_submit_Base::C_Data::GetEntrys(), CSeq_submit_Base::C_Data::IsEntrys(), m_CurrentNode, ParseObject(), and PushNode().

ParseStream()

void CDiscrepancyContext::ParseStream ( CObjectIStream &  stream, const string &  fname, bool  skip, const string &  default_header = kEmptyStr  )

overridevirtual

Implements CDiscrepancySet.

Definition at line 195 of file discrepancy_stream.cpp.

References CReadHook_Bioseq, CReadHook_Bioseq_set, CReadHook_Bioseq_set_class, eFile, CObjectIStream::EndOfData(), CObjectIStream::eNoFileHeader, eNone, eSubmit, eUnknown, Extend(), CObjectTypeInfo::FindMember(), CObjectIStream::GetStreamPos(), m_CurrentNode, m_RootNode, m_Skip, NCBI_THROW, ObjectInfo(), PopNode(), PushNode(), CObjectIStream::Read(), CObjectIStream::ReadFileHeader(), CObjectTypeInfoMI::SetLocalReadHook(), CObjectTypeInfo::SetLocalReadHook(), and CObjectIStream::SetStreamPos().

ParseStrings()

void CDiscrepancyContext::ParseStrings ( const string &  fname )

overridevirtual

Implements CDiscrepancySet.

Definition at line 174 of file discrepancy_stream.cpp.

References CStreamLineReader::AtEOF(), eFile, eString, eUnknown, m_CurrentNode, m_RootNode, NCBI_THROW, PopNode(), PushNode(), and RunTests().

PopNode()

void CDiscrepancyContext::PopNode ( )

inlineprotected

Definition at line 820 of file discrepancy_core.hpp.

References m_CurrentNode.

Referenced by AutofixBioseq_set(), AutofixFile(), CCopyHook_Bioseq_set::CopyObject(), CCopyHook_Bioseq::CopyObject(), ParseStream(), ParseStrings(), CReadHook_Bioseq_set::ReadObject(), and CReadHook_Bioseq::ReadObject().

Populate()

void CDiscrepancyContext::Populate ( CParseNode &  node )

protected

Definition at line 382 of file discrepancy_stream.cpp.

References eBioseq, eSeqSet, eSeqSet_Funny, eSeqSet_Genome, eSeqSet_GenProd, eSeqSet_NucProt, eSeqSet_SegSet, eSubmit, CDiscrepancyContext::CParseNode::m_Type, PopulateBioseq(), PopulateSeqSet(), and PopulateSubmit().

Referenced by Extend(), and ParseAll().

PopulateBioseq()

void CDiscrepancyContext::PopulateBioseq ( CParseNode &  node )

protected

Definition at line 418 of file discrepancy_stream.cpp.

References CDiscrepancyContext::CParseNode::AddDescriptor(), CDiscrepancyContext::CParseNode::AddFeature(), BuildSeqSummary(), CSeq_descr_Base::CanGet(), CBioseq_Base::CanGetDescr(), eSeqSet_Funny, eSeqSet_Genome, eSeqSet_NucProt, eSeqSet_SegSet, eSubmit, CSeq_descr_Base::Get(), CBioseq_Base::GetAnnot(), CBioseq_Base::GetDescr(), IsSeqSet(), CBioseq_Base::IsSetAnnot(), label, CDiscrepancyContext::CParseNode::m_BioseqSummary, CDiscrepancyContext::CParseNode::m_Biosource, CDiscrepancyContext::CParseNode::m_Molinfo, CDiscrepancyContext::CParseNode::m_Obj, CDiscrepancyContext::CParseNode::m_Parent, CDiscrepancyContext::CParseNode::m_Ref, CDiscrepancyContext::CParseNode::m_Title, n, and CConstRef< C, Locker >::Reset().

Referenced by Populate().

PopulateSeqSet()

void CDiscrepancyContext::PopulateSeqSet ( CParseNode &  node )

protected

Definition at line 465 of file discrepancy_stream.cpp.

References CDiscrepancyContext::CParseNode::AddDescriptor(), CDiscrepancyContext::CParseNode::AddFeature(), CSeq_descr_Base::CanGet(), CBioseq_set_Base::CanGetDescr(), eSeqSet_Genome, CSeq_descr_Base::Get(), CBioseq_set_Base::GetAnnot(), CBioseq_set_Base::GetDescr(), IsSeqSet(), CBioseq_set_Base::IsSetAnnot(), CDiscrepancyContext::CParseNode::m_Biosource, CDiscrepancyContext::CParseNode::m_Molinfo, CDiscrepancyContext::CParseNode::m_Obj, CDiscrepancyContext::CParseNode::m_Title, n, and CConstRef< C, Locker >::Reset().

Referenced by Populate().

PopulateSubmit()

void CDiscrepancyContext::PopulateSubmit ( CParseNode &  node )

protected

Definition at line 405 of file discrepancy_stream.cpp.

References CCit_sub_Base::CanGetAuthors(), CCit_sub_Base::GetAuthors(), CSubmit_block_Base::GetCit(), CSeq_submit_Base::GetSub(), CSubmit_block_Base::IsSetCit(), CSeq_submit_Base::IsSetSub(), CDiscrepancyContext::CParseNode::m_AuthorMap, CDiscrepancyContext::CParseNode::m_Authors, and CDiscrepancyContext::CParseNode::m_Obj.

Referenced by Populate().

ProdForFeature()

string CDiscrepancyContext::ProdForFeature ( const CParseNode &  node )

protected

Definition at line 578 of file discrepancy_context.cpp.

References CDiscrepancyContext::CParseNode::eKnownProduct, GetProductName(), CDiscrepancyContext::CParseNode::m_Info, CDiscrepancyContext::CParseNode::m_Obj, CDiscrepancyContext::CParseNode::m_Product, and m_Scope.

Referenced by GetProdForFeature().

PropagateFlags()

void CDiscrepancyContext::PropagateFlags ( unsigned char  f )

inline

Definition at line 373 of file discrepancy_core.hpp.

References f(), and m_CurrentNode.

PubdescObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::PubdescObjRef	(	const CPubdesc &	pubdesc,
		bool	fix = false,
		const CObject *	more = nullptr
	)

Definition at line 917 of file discrepancy_context.cpp.

References _ASSERT, CDiscrepancyObject, eSeqDesc, eSeqFeat, CDiscrepancyObject::GetTextObjectDescription(), m_CurrentNode, m_Scope, and CRef< C, Locker >::Reset().

Push()

void CDiscrepancyContext::Push ( const CSerialObject &  root, const string &  fname  )

overridevirtual

Implements CDiscrepancySet.

Definition at line 556 of file discrepancy_core.cpp.

References eFile, eNone, eUnknown, CSerialObject::GetThisTypeInfo(), m_CurrentNode, m_NodeMap, m_RootNode, NCBI_THROW, and ParseObject().

Referenced by Parse().

PushNode()

void CDiscrepancyContext::PushNode ( EObjType  type )

protected

Definition at line 159 of file discrepancy_stream.cpp.

References m_CurrentNode.

Referenced by AutofixBioseq_set(), AutofixFile(), CCopyHook_Bioseq_set::CopyObject(), CCopyHook_Bioseq::CopyObject(), ParseObject(), ParseStream(), ParseStrings(), CReadHook_Bioseq_set::ReadObject(), and CReadHook_Bioseq::ReadObject().

ReadFlags()

unsigned char CDiscrepancyContext::ReadFlags ( ) const

inline

Definition at line 372 of file discrepancy_core.hpp.

References m_CurrentNode.

ReplaceObject()

void CDiscrepancyContext::ReplaceObject	(	CReportObj &	obj,
		CSerialObject *	ser,
		bool	alt = false
	)

Definition at line 537 of file discrepancy_stream.cpp.

References FindNode(), CDiscrepancyObject::m_Fix, CDiscrepancyContext::CParseNode::m_Obj, CDiscrepancyObject::m_Ref, and CConstRef< C, Locker >::Reset().

Referenced by ReplaceSeq_feat().

ReplaceSeq_feat()

void CDiscrepancyContext::ReplaceSeq_feat	(	CReportObj &	obj,
		const CSeq_feat &	old_feat,
		CSeq_feat &	new_feat,
		bool	alt = false
	)

Definition at line 545 of file discrepancy_stream.cpp.

References ftable, GetScope(), m_AF_Seq_annot, CSeq_feat_EditHandle::Replace(), ReplaceObject(), and CSeq_annot_Base::SetData().

RunTests() [1/2]

void CDiscrepancyContext::RunTests ( )

protected

Definition at line 719 of file discrepancy_core.cpp.

References _ASSERT, ClearFeatureList(), CollectFeature(), eBioseq, eFile, eNone, ERR_POST, eString, eSubmit, eUnknown, GetAllFeat(), Info(), IsSeqSet(), m_All_AUTHORS, m_All_BIOSRC, m_All_DESC, m_All_FEAT, m_All_PUBDESC, m_All_SEQ_SET, m_All_SEQUENCE, m_All_STRING, m_All_SUBMIT, m_CurrentNode, NCBI_THROW, and test.

Referenced by Extend(), ParseAll(), and ParseStrings().

RunTests() [2/2]

CRef< CDiscrepancyProduct > CDiscrepancyContext::RunTests ( const TTestNamesSet &  testnames, const CSerialObject &  object, const string &  filename  )

overridevirtual

Implements CDiscrepancySet.

Definition at line 964 of file discrepancy_context.cpp.

References AddTest(), GetProduct(), n, and Parse().

SeqdescObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::SeqdescObjRef	(	const CSeqdesc &	desc,
		const CObject *	fix = nullptr,
		const CObject *	more = nullptr
	)

Definition at line 881 of file discrepancy_context.cpp.

References CDiscrepancyObject, FindNode(), CDiscrepancyObject::GetTextObjectDescription(), and CRef< C, Locker >::Reset().

SeqFeatObjRef() [1/2]

CRef< CDiscrepancyObject > CDiscrepancyContext::SeqFeatObjRef	(	const CSeq_feat &	feat,
		const CObject *	fix,
		const CObject *	more = nullptr
	)

Definition at line 867 of file discrepancy_context.cpp.

References CDiscrepancyObject, FindNode(), CDiscrepancyObject::GetTextObjectDescription(), m_Scope, and CRef< C, Locker >::Reset().

SeqFeatObjRef() [2/2]

CRef< CDiscrepancyObject > CDiscrepancyContext::SeqFeatObjRef	(	const CSeq_feat &	feat,
		EFixType	fix = eFixNone,
		const CObject *	more = nullptr
	)

Definition at line 843 of file discrepancy_context.cpp.

References CDiscrepancyObject, ContainingSet(), eFixParent, eFixSelf, eFixSet, FindNode(), CDiscrepancyObject::GetTextObjectDescription(), CDiscrepancyContext::CRefNode::m_Parent, m_Scope, and CRef< C, Locker >::Reset().

SetSuspectRules()

void CDiscrepancyContext::SetSuspectRules ( const string &  name, bool  read = true  )

overridevirtual

Implements CDiscrepancySet.

Definition at line 64 of file discrepancy_context.cpp.

References GetProductRules(), m_ProductRules, and m_SuspectRules.

Skip()

bool CDiscrepancyContext::Skip ( void  )

protected

Definition at line 167 of file discrepancy_stream.cpp.

References eSeqSet, m_CurrentNode, and m_Skip.

Referenced by CReadHook_Bioseq_set::ReadObject(), and CReadHook_Bioseq::ReadObject().

StringObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::StringObjRef	(	const CObject *	fix = nullptr,
		const CObject *	more = nullptr
	)

Definition at line 956 of file discrepancy_context.cpp.

References CDiscrepancyObject, FindNode(), m_CurrentNode, and CRef< C, Locker >::Reset().

SubmitBlockObjRef()

CRef< CDiscrepancyObject > CDiscrepancyContext::SubmitBlockObjRef	(	bool	fix = false,
		const CObject *	more = nullptr
	)

Definition at line 835 of file discrepancy_context.cpp.

References _ASSERT, CDiscrepancyObject, eSubmit, and m_CurrentNode.

Summarize()

unsigned CDiscrepancyContext::Summarize ( )

overridevirtual

Implements CDiscrepancySet.

Definition at line 607 of file discrepancy_core.cpp.

References m_Tests, and test.

TypeName()

static string CDiscrepancyContext::TypeName ( EObjType  n )

inlinestaticprotected

Definition at line 664 of file discrepancy_core.hpp.

References n, and names.

Referenced by CDiscrepancyContext::CRefNode::GetText(), and CDiscrepancyContext::CParseNode::Path().

Friends And Related Function Documentation

CCopyHook_Bioseq

friend class CCopyHook_Bioseq

friend

Definition at line 629 of file discrepancy_core.hpp.

Referenced by AutofixFile().

CCopyHook_Bioseq_set

friend class CCopyHook_Bioseq_set

friend

Definition at line 628 of file discrepancy_core.hpp.

Referenced by AutofixFile().

CCopyHook_Seq_annot

friend class CCopyHook_Seq_annot

friend

Definition at line 631 of file discrepancy_core.hpp.

Referenced by AutofixFile().

CCopyHook_Seq_descr

friend class CCopyHook_Seq_descr

friend

Definition at line 630 of file discrepancy_core.hpp.

Referenced by AutofixFile().

CCopyHook_Submit_block

friend class CCopyHook_Submit_block

friend

Definition at line 632 of file discrepancy_core.hpp.

Referenced by AutofixFile().

CDiscrepancyObject

friend class CDiscrepancyObject

friend

Definition at line 830 of file discrepancy_core.hpp.

Referenced by AuthorsObjRef(), BioseqObjRef(), BioseqSetObjRef(), BiosourceObjRef(), PubdescObjRef(), SeqdescObjRef(), SeqFeatObjRef(), StringObjRef(), and SubmitBlockObjRef().

CReadHook_Bioseq

friend class CReadHook_Bioseq

friend

Definition at line 627 of file discrepancy_core.hpp.

Referenced by ParseStream().

CReadHook_Bioseq_set

friend class CReadHook_Bioseq_set

friend

BIG FILE.

Definition at line 625 of file discrepancy_core.hpp.

Referenced by ParseStream().

CReadHook_Bioseq_set_class

friend class CReadHook_Bioseq_set_class

friend

Definition at line 626 of file discrepancy_core.hpp.

Referenced by ParseStream().

Member Data Documentation

m_AF_Bioseq

CRef<CBioseq> CDiscrepancyContext::m_AF_Bioseq

protected

Definition at line 605 of file discrepancy_core.hpp.

Referenced by CCopyHook_Bioseq::CopyObject().

m_AF_Bioseq_set

CRef<CBioseq_set> CDiscrepancyContext::m_AF_Bioseq_set

protected

Definition at line 604 of file discrepancy_core.hpp.

Referenced by CCopyHook_Bioseq_set::CopyObject().

m_AF_Seq_annot

CRef<CSeq_annot> CDiscrepancyContext::m_AF_Seq_annot

protected

Definition at line 606 of file discrepancy_core.hpp.

Referenced by AutofixSeq_annot(), CCopyHook_Seq_annot::CopyObject(), and ReplaceSeq_feat().

m_AF_Seq_descr

CRef<CSeq_descr> CDiscrepancyContext::m_AF_Seq_descr

protected

Definition at line 607 of file discrepancy_core.hpp.

Referenced by AutofixSeq_descr(), and CCopyHook_Seq_descr::CopyObject().

m_AF_Submit_block

CRef<CSubmit_block> CDiscrepancyContext::m_AF_Submit_block

protected

Definition at line 608 of file discrepancy_core.hpp.

Referenced by AutofixSubmit_block(), and CCopyHook_Submit_block::CopyObject().

m_All_AUTHORS

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_AUTHORS

protected

Definition at line 619 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_BIOSRC

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_BIOSRC

protected

Definition at line 617 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_DESC

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_DESC

protected

Definition at line 616 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_FEAT

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_FEAT

protected

Definition at line 615 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_PUBDESC

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_PUBDESC

protected

Definition at line 618 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_SEQ_SET

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_SEQ_SET

protected

Definition at line 614 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_SEQUENCE

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_SEQUENCE

protected

Definition at line 613 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_STRING

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_STRING

protected

Definition at line 621 of file discrepancy_core.hpp.

Referenced by RunTests().

m_All_SUBMIT

vector<CDiscrepancyCore*> CDiscrepancyContext::m_All_SUBMIT

protected

Definition at line 620 of file discrepancy_core.hpp.

Referenced by RunTests().

m_Bioseq_set_Stack

vector<CConstRef<CBioseq_set> > CDiscrepancyContext::m_Bioseq_set_Stack

protected

Definition at line 555 of file discrepancy_core.hpp.

m_Current_Bioseq

CConstRef<CBioseq> CDiscrepancyContext::m_Current_Bioseq

protected

Definition at line 557 of file discrepancy_core.hpp.

m_Current_Bioseq_Handle

CBioseq_Handle CDiscrepancyContext::m_Current_Bioseq_Handle

protected

Definition at line 556 of file discrepancy_core.hpp.

m_Current_Cit_sub_StringObj

CRef<CSimpleTypeObject<string> > CDiscrepancyContext::m_Current_Cit_sub_StringObj

protected

Definition at line 560 of file discrepancy_core.hpp.

m_Current_Pub

CConstRef<CPub> CDiscrepancyContext::m_Current_Pub

protected

Definition at line 563 of file discrepancy_core.hpp.

m_Current_Pub_equiv

CConstRef<CPub_equiv> CDiscrepancyContext::m_Current_Pub_equiv

protected

Definition at line 564 of file discrepancy_core.hpp.

m_Current_Seq_feat

CConstRef<CSeq_feat> CDiscrepancyContext::m_Current_Seq_feat

protected

Definition at line 562 of file discrepancy_core.hpp.

m_Current_Seqdesc

CConstRef<CSeqdesc> CDiscrepancyContext::m_Current_Seqdesc

protected

Definition at line 561 of file discrepancy_core.hpp.

m_Current_Submit_block

CConstRef<CSubmit_block> CDiscrepancyContext::m_Current_Submit_block

protected

Definition at line 558 of file discrepancy_core.hpp.

m_Current_Submit_block_StringObj

CRef<CSimpleTypeObject<string> > CDiscrepancyContext::m_Current_Submit_block_StringObj

protected

Definition at line 559 of file discrepancy_core.hpp.

m_CurrentNode

CRef<CParseNode> CDiscrepancyContext::m_CurrentNode

protected

Definition at line 824 of file discrepancy_core.hpp.

Referenced by AuthorsObjRef(), AuthPub(), AutofixBioseq(), AutofixBioseq_set(), AutofixFile(), AutofixSeq_annot(), AutofixSeq_descr(), BioseqObjRef(), BioseqSetObjRef(), BiosourceObjRef(), CanFixBioseq(), CanFixBioseq_set(), CanFixDesc(), CanFixFeat(), CanFixSubmit_block(), CCopyHook_Bioseq_set::CopyObject(), CCopyHook_Bioseq::CopyObject(), CurrentBioseq(), CurrentBioseq_set(), CurrentText(), Extend(), FindNode(), GetAllFeat(), GetAllSeqdesc(), GetAuthors(), GetBiosource(), GetBiosources(), GetFeat(), GetMolinfo(), GetPerson_id(), GetPubdescs(), GetSeqdesc(), GetSeqSummary(), GetSetBiosources(), GetSubmit_block(), GetTitle(), InGenProdSet(), IsBioseq(), ParseAll(), ParseObject(), ParseStream(), ParseStrings(), PopNode(), PropagateFlags(), PubdescObjRef(), Push(), PushNode(), CReadHook_Bioseq_set_class::ReadClassMember(), ReadFlags(), CReadHook_Bioseq_set::ReadObject(), CReadHook_Bioseq::ReadObject(), RunTests(), Skip(), StringObjRef(), and SubmitBlockObjRef().

m_Enabled

ct::const_bitset<static_cast<size_t>eTestTypes::max_num_types), eTestTypes> CDiscrepancyContext::m_Enabled

protected

Definition at line 610 of file discrepancy_core.hpp.

Referenced by AddTest().

m_Feat_RNAs

vector<const CSeq_feat*> CDiscrepancyContext::m_Feat_RNAs

protected

Definition at line 575 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and Feat_RNAs().

m_FeatAll

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatAll

protected

Definition at line 568 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatAll().

m_FeatCDS

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatCDS

protected

Definition at line 571 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatCDS().

m_FeatExons

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatExons

protected

Definition at line 576 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatExons().

m_FeatGenes

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatGenes

protected

Definition at line 569 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatGenes().

m_FeatIntrons

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatIntrons

protected

Definition at line 577 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatIntrons().

m_FeatMisc

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatMisc

protected

Definition at line 578 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatMisc().

m_FeatMRNAs

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatMRNAs

protected

Definition at line 572 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatMRNAs().

m_FeatPseudo

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatPseudo

protected

Definition at line 570 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatPseudo().

m_FeatRRNAs

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatRRNAs

protected

Definition at line 573 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatRRNAs().

m_FeatTree

CRef<feature::CFeatTree> CDiscrepancyContext::m_FeatTree

protected

Definition at line 553 of file discrepancy_core.hpp.

Referenced by CCopyHook_Bioseq_set::CopyObject(), CCopyHook_Bioseq::CopyObject(), and Extend().

m_FeatTRNAs

vector<const CSeq_feat*> CDiscrepancyContext::m_FeatTRNAs

protected

Definition at line 574 of file discrepancy_core.hpp.

Referenced by ClearFeatureList(), CollectFeature(), and FeatTRNAs().

m_Fixes

vector<CDiscrepancyObject*>* CDiscrepancyContext::m_Fixes

protected

Definition at line 580 of file discrepancy_core.hpp.

Referenced by AutofixBioseq(), AutofixBioseq_set(), AutofixFile(), AutofixSeq_annot(), AutofixSeq_descr(), AutofixSubmit_block(), CanFixBioseq(), CanFixBioseq_set(), CanFixSeq_annot(), CanFixSeqdesc(), and CanFixSubmit_block().

m_NodeMap

map<const CRefNode*, CParseNode*> CDiscrepancyContext::m_NodeMap

protected

Definition at line 579 of file discrepancy_core.hpp.

Referenced by AutofixBioseq(), AutofixBioseq_set(), AutofixSeq_annot(), AutofixSeq_descr(), AutofixSubmit_block(), FindNode(), and Push().

m_OrganelleProductRules

CConstRef<CSuspect_rule_set> CDiscrepancyContext::m_OrganelleProductRules

protected

Definition at line 566 of file discrepancy_core.hpp.

Referenced by GetOrganelleProductRules().

m_ProductRules

CConstRef<CSuspect_rule_set> CDiscrepancyContext::m_ProductRules

protected

Definition at line 565 of file discrepancy_core.hpp.

Referenced by GetProductRules(), and SetSuspectRules().

m_RootNode

CRef<CParseNode> CDiscrepancyContext::m_RootNode

protected

Definition at line 823 of file discrepancy_core.hpp.

Referenced by AutofixFile(), Parse(), ParseStream(), ParseStrings(), and Push().

m_Scope

CRef<objects::CScope> CDiscrepancyContext::m_Scope

protected

Definition at line 552 of file discrepancy_core.hpp.

Referenced by AuthorsObjRef(), BiosourceObjRef(), CCopyHook_Bioseq_set::CopyObject(), CCopyHook_Bioseq::CopyObject(), Extend(), GeneForFeature(), GetBioseq_setHandle(), GetBioseqHandle(), IsBGPipe(), ProdForFeature(), PubdescObjRef(), and SeqFeatObjRef().

m_Skip

bool CDiscrepancyContext::m_Skip

protected

Definition at line 822 of file discrepancy_core.hpp.

Referenced by ParseStream(), and Skip().

m_SuspectRules

string CDiscrepancyContext::m_SuspectRules

protected

Definition at line 567 of file discrepancy_core.hpp.

Referenced by GetProductRules(), and SetSuspectRules().

m_Tests

TDiscrepancyCoreMap CDiscrepancyContext::m_Tests

protected

Definition at line 554 of file discrepancy_core.hpp.

Referenced by AddTest(), Autofix(), GetProduct(), GetTests(), and Summarize().

---

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

• src/misc/discrepancy/discrepancy_core.hpp
• src/misc/discrepancy/discrepancy_context.cpp
• src/misc/discrepancy/discrepancy_core.cpp
• src/misc/discrepancy/discrepancy_stream.cpp