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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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CDiscrepancyContext (objects::CScope &scope)
 
CRef< CDiscrepancyProductRunTests (const TTestNamesSet &testnames, const CSerialObject &object, const string &filename) override
 
CRef< CDiscrepancyProductGetProduct () 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
 
CParseNodeFindNode (const CRefNode &obj)
 
const CObjectGetMore (CReportObj &obj)
 
const CSerialObjectFindObject (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 stringCurrentText () const
 
const CBioseqCurrentBioseq () const
 
const CBioseq_setCurrentBioseq_set () const
 
const CSeqSummaryCurrentBioseqSummary () 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_setGetProductRules ()
 
CConstRef< CSuspect_rule_setGetOrganelleProductRules ()
 
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 CSeqSummaryGetSeqSummary ()
 
void BuildSeqSummary (const CBioseq &bs, CSeqSummary &summary)
 
bool InGenProdSet () const
 
CConstRef< CSeqdescGetTitle () const
 
CConstRef< CSeqdescGetMolinfo () const
 
CConstRef< CSeqdescGetBiosource () 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_featGetGeneForFeature (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
 
CRefNodeContainingSet (CRefNode &ref)
 
CRef< CDiscrepancyObjectBioseqObjRef (EFixType fix=eFixNone, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectBioseqSetObjRef (bool fix=false, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectSubmitBlockObjRef (bool fix=false, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectSeqFeatObjRef (const CSeq_feat &feat, EFixType fix=eFixNone, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectSeqFeatObjRef (const CSeq_feat &feat, const CObject *fix, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectSeqdescObjRef (const CSeqdesc &desc, const CObject *fix=nullptr, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectBiosourceObjRef (const CBioSource &biosrc, bool fix=false, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectPubdescObjRef (const CPubdesc &pubdesc, bool fix=false, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectAuthorsObjRef (const CAuth_list &authors, bool fix=false, const CObject *more=nullptr)
 
CRef< CDiscrepancyObjectStringObjRef (const CObject *fix=nullptr, const CObject *more=nullptr)
 
bool IsBioseq () const
 
const CPubAuthPub (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_idGetPerson_id () const
 
const CSubmit_blockGetSubmit_block () const
 
- Public Member Functions inherited from CDiscrepancySet
virtual ~CDiscrepancySet ()
 
void SetUserData (void *p)
 
void * GetUserData () const
 
const stringGetLineage () 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...
 
CObjectoperator= (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< CDiscrepancySetNew (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

CParseNodeFindLocalNode (const CParseNode &node, const CSeq_feat &feat) const
 
CParseNodeFindNode (const CObject *obj) const
 
CParseNodeFindNode (const CSeq_feat &feat) const
 
CParseNodeFindNode (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 CParseNodeGeneForFeature (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< CBioseqm_Current_Bioseq
 
CConstRef< CSubmit_blockm_Current_Submit_block
 
CRef< CSimpleTypeObject< string > > m_Current_Submit_block_StringObj
 
CRef< CSimpleTypeObject< string > > m_Current_Cit_sub_StringObj
 
CConstRef< CSeqdescm_Current_Seqdesc
 
CConstRef< CSeq_featm_Current_Seq_feat
 
CConstRef< CPubm_Current_Pub
 
CConstRef< CPub_equivm_Current_Pub_equiv
 
CConstRef< CSuspect_rule_setm_ProductRules
 
CConstRef< CSuspect_rule_setm_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_setm_AF_Bioseq_set
 
CRef< CBioseqm_AF_Bioseq
 
CRef< CSeq_annotm_AF_Seq_annot
 
CRef< CSeq_descrm_AF_Seq_descr
 
CRef< CSubmit_blockm_AF_Submit_block
 
ct::const_bitset< static_cast< size_t >eTestTypes::max_num_types), eTestTypesm_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< CParseNodem_RootNode
 
CRef< CParseNodem_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< boolm_Gui = false
 

Detailed Description

Definition at line 322 of file discrepancy_core.hpp.

Member Enumeration Documentation

◆ EFixType

BIG FILE.

Enumerator
eFixNone 
eFixSelf 
eFixParent 
eFixSet 

Definition at line 423 of file discrepancy_core.hpp.

◆ EFlag

Enumerator
eHasRearranged 
eHasSatFeat 
eHasNonSatFeat 

Definition at line 329 of file discrepancy_core.hpp.

◆ EObjType

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

◆ 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 
)

◆ 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

◆ Autofix() [2/2]

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

◆ AutofixBioseq()

void CDiscrepancyContext::AutofixBioseq ( )
protected

◆ AutofixBioseq_set()

void CDiscrepancyContext::AutofixBioseq_set ( )
protected

◆ AutofixFile()

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

◆ AutofixSeq_annot()

void CDiscrepancyContext::AutofixSeq_annot ( )
protected

◆ AutofixSeq_descr()

void CDiscrepancyContext::AutofixSeq_descr ( )
protected

◆ AutofixSubmit_block()

void CDiscrepancyContext::AutofixSubmit_block ( )
protected

◆ BioseqObjRef()

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

◆ 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 
)

◆ BuildSeqSummary()

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

◆ 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

◆ 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

◆ CanFixDesc()

bool CDiscrepancyContext::CanFixDesc ( CRefNode refnode)
protected

◆ CanFixFeat()

bool CDiscrepancyContext::CanFixFeat ( CRefNode refnode)
protected

◆ 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

◆ ClearFeatureList()

void CDiscrepancyContext::ClearFeatureList ( )

◆ CollectFeature()

void CDiscrepancyContext::CollectFeature ( const CSeq_feat feat)

◆ Compare()

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

◆ CompareRefs()

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

◆ ContainingSet()

CDiscrepancyContext::CRefNode * CDiscrepancyContext::ContainingSet ( CDiscrepancyContext::CRefNode ref)

◆ 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

◆ 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)

◆ FindNode() [3/4]

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

◆ FindNode() [4/4]

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

◆ FindObject()

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

◆ GeneForFeature()

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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ InNucProtSet()

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

◆ 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 ( )

◆ 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

◆ IsOrganelle()

bool CDiscrepancyContext::IsOrganelle ( const CBioSource biosrc)
static

◆ IsPseudo() [1/2]

bool CDiscrepancyContext::IsPseudo ( const CParseNode node)
protected

◆ 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

◆ IsSeqSet()

static bool CDiscrepancyContext::IsSeqSet ( EObjType  n)
inlinestaticprotected

◆ 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

◆ 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)

◆ ParseObject() [3/4]

void CDiscrepancyContext::ParseObject ( const CSeq_entry root)

◆ ParseObject() [4/4]

void CDiscrepancyContext::ParseObject ( const CSeq_submit root)

◆ ParseStream()

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

◆ ParseStrings()

void CDiscrepancyContext::ParseStrings ( const string fname)
overridevirtual

◆ PopNode()

void CDiscrepancyContext::PopNode ( )
inlineprotected

◆ Populate()

void CDiscrepancyContext::Populate ( CParseNode node)
protected

◆ PopulateBioseq()

void CDiscrepancyContext::PopulateBioseq ( CParseNode node)
protected

◆ PopulateSeqSet()

void CDiscrepancyContext::PopulateSeqSet ( CParseNode node)
protected

◆ PopulateSubmit()

void CDiscrepancyContext::PopulateSubmit ( CParseNode node)
protected

◆ ProdForFeature()

string CDiscrepancyContext::ProdForFeature ( const CParseNode node)
protected

◆ 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 
)

◆ Push()

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

◆ PushNode()

void CDiscrepancyContext::PushNode ( EObjType  type)
protected

◆ 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 
)

◆ ReplaceSeq_feat()

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

◆ RunTests() [1/2]

void CDiscrepancyContext::RunTests ( )
protected

◆ 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 
)

◆ SeqFeatObjRef() [1/2]

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

◆ SeqFeatObjRef() [2/2]

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

◆ 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

◆ StringObjRef()

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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ m_NodeMap

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

◆ 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

◆ 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:
Modified on Tue May 28 05:53:48 2024 by modify_doxy.py rev. 669887