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NCBI C++ ToolKit: src/misc/discrepancy/discrepancy_core.hpp Source File

std::initializer_list<const char*>*

;

<eTestNames _Name>

eTestNames

()

{

m_props->Name; }

string_view

()

{

m_props->sName; }

()

{

m_Objs.empty(); }

<eTestNames _Name>

<eTestNames _Name>

vector<pair<size_t, size_t>>

;

list<pair<CRef<CDiscrepancyObject>,

>>

;

Summarize()

;

eHasRearranged = 1 << 0,

eHasSatFeat = 1 << 1,

eHasNonSatFeat = 1 << 2

AddTest(eTestNames name)

;

AddTest(string_view name)

;

Push(

& root,

& fname)

;

()

{ ParseAll(*m_RootNode); }

Parse(

& root,

& fname);

ParseObject(

& root);

ParseStream(

& stream,

& fname,

skip,

& default_header =

)

;

ParseStrings(

& fname)

;

Summarize()

;

AutofixFile(vector<CDiscrepancyObject*>&fixes,

& default_header);

CParseNode* FindNode(

CRefNode& obj);

&

()

{

m_CurrentNode->m_Ref->m_Text; }

()

{

m_CurrentNode->m_Flags; }

objects::CScope&

()

{

objects::CScope&

(*m_Scope); }

SetSuspectRules(

& name,

read =

)

;

IsUnculturedNonOrganelleName(

& taxname);

HasLineage(

& biosrc,

& def_lineage,

&

);

HasLineage(

* biosrc,

& lineage)

;

IsEukaryotic(

* biosrc)

;

IsProkaryotic(

* biosrc)

;

IsBacterial(

* biosrc)

;

IsViral(

* biosrc)

;

vector<CConstRef<CSeqdesc>>&

()

{

m_CurrentNode->m_SetBiosources; }

GetGenomeName(

);

GetAminoacidName(

& feat);

IsBadLocusTagFormat(string_view locus_tag);

IsRefseq()

;

GetProdForFeature(

& feat);

CollectFeature(

& feat);

ClearFeatureList();

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; }

CRefNode* ContainingSet(CRefNode& ref);

*

(

*

)

{

& apm = m_CurrentNode->m_AuthorPubMap;

it = apm.find(

);

it == apm.end() ?

: it->second; }

node = follow ? node->

:

;

node = follow ? node->

:

;

vector<const CBioSource*>&

()

{

m_CurrentNode->m_Biosources; }

vector<const CPubdesc*>&

()

{

m_CurrentNode->m_Pubdescs; }

vector<const CAuth_list*>&

()

{

m_CurrentNode->m_Authors; }

CanFixBioseq_set();

CanFixSeq_annot();

CanFixSeqdesc();

CanFixSubmit_block();

CanFixBioseq(

& refnode);

CanFixBioseq_set(

& refnode);

CanFixFeat(

& refnode);

CanFixDesc(

& refnode);

CanFixSubmit_block(

& refnode);

AutofixBioseq();

AutofixBioseq_set();

AutofixSeq_annot();

AutofixSeq_descr();

AutofixSubmit_block();

eSeqSet_NucProt:

eSeqSet_GenProd:

*

[] =

GetText()

;

GetBioseqLabel()

;

eKnownPseudo = 1 << 1,

eKnownProduct = 1 << 3

m_Ref->m_Parent.Reset(parent->m_Ref);

new_node->m_Obj = &seqdesc;

m_Descriptors.push_back(new_node);

m_DescriptorMap[&seqdesc] = new_node;

m_Biosources.push_back(biosrc);

m_BiosourceMap[biosrc] = new_node;

(seqdesc.

()) {

m_Pubdescs.push_back(pub);

m_PubdescMap[pub] = new_node;

(

& it : pub->

().

()) {

(it->IsSetAuthors()) {

m_Authors.push_back(auth);

m_AuthorMap[auth] = new_node;

m_AuthorPubMap[auth] = &*it;

new_node->m_Obj = &feat;

m_Features.push_back(new_node);

m_FeatureMap[&feat] = new_node;

m_Biosources.push_back(biosrc);

m_BiosourceMap[biosrc] = new_node;

m_Pubdescs.push_back(pub);

m_PubdescMap[pub] = new_node;

(

& it : pub->

().

()) {

(it->IsSetAuthors()) {

m_Authors.push_back(auth);

m_AuthorMap[auth] = new_node;

m_AuthorPubMap[auth] = &*it;

()

{

m_Type == eSeqSet_GenProd ?

: m_Parent ? m_Parent->InGenProdSet() :

; }

() {

m_Parent ? m_Parent->

() +

+ TypeName(m_Type) +

+ to_string(m_Index) : TypeName(m_Type) +

+ to_string(m_Index); }

ParseAll(CParseNode& node);

Populate(CParseNode& node);

PopulateBioseq(CParseNode& node);

PopulateSeqSet(CParseNode& node);

PopulateSubmit(CParseNode& node);

PushNode(EObjType);

() { m_CurrentNode.Reset(m_CurrentNode->m_Parent); }

ProdForFeature(

& node);

: m_Ref(ref), m_Fix(fix), m_More(more) {}

()

{

m_Ref->GetBioseqLabel(); }

()

{

m_Ref->GetText(); }

(

ref = m_Ref; ref; ref = ref->m_Parent) {

GetFeatureType()

;

GetLocation()

;

(m_Ref->m_Type) {

()

{

m_Fix && !m_Fixed; }

()

{

m_Fixed; }

m_Fixed {

};

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@Auth_list.hpp User-defined methods of the data storage class.

static const CDiscrepancyCaseProps * props

virtual TReportObjectList GetObjects() const =0

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

CRef< CBioseq > m_AF_Bioseq

vector< CDiscrepancyObject * > * m_Fixes

CSeqdesc_run GetAllSeqdesc()

CConstRef< CSeqdesc > m_Current_Seqdesc

CRef< CSeq_descr > m_AF_Seq_descr

const vector< const CSeq_feat * > & FeatTRNAs()

vector< const CSeq_feat * > m_Feat_RNAs

const vector< const CSeq_feat * > & FeatExons()

unsigned char ReadFlags() const

CRef< objects::CScope > m_Scope

const string & CurrentText() const

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

CDiscrepancyContext(objects::CScope &scope)

TDiscrepancyCoreMap m_Tests

CRef< CBioseq_set > m_AF_Bioseq_set

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

CRef< CSimpleTypeObject< string > > m_Current_Submit_block_StringObj

CRef< CParseNode > m_RootNode

CRef< feature::CFeatTree > m_FeatTree

CConstRef< CPub > m_Current_Pub

const vector< const CSeq_feat * > & FeatGenes()

CRef< CParseNode > m_CurrentNode

vector< const CSeq_feat * > m_FeatAll

CConstRef< CSubmit_block > m_Current_Submit_block

bool InGenProdSet() const

vector< const CSeq_feat * > m_FeatRRNAs

CConstRef< CSeqdesc > GetTitle() const

objects::CScope & GetScope() const

CConstRef< CSeq_feat > m_Current_Seq_feat

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

vector< const CSeq_feat * > m_FeatCDS

const vector< const CSeq_feat * > & FeatMRNAs()

const CPub * AuthPub(const CAuth_list *a) const

CConstRef< CBioseq > m_Current_Bioseq

const CSeqSummary & GetSeqSummary()

CBioseq_Handle m_Current_Bioseq_Handle

static bool InGenProdSet(const CParseNode *node)

const vector< const CAuth_list * > & GetAuthors() const

const vector< const CSeq_feat * > & Feat_RNAs()

CSeq_feat_run GetAllFeat()

const vector< const CSeq_feat * > & FeatPseudo()

const CBioseq & CurrentBioseq() const

vector< const CSeq_feat * > m_FeatGenes

static string TypeName(EObjType n)

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &bss)

CConstRef< CSeqdesc > GetBiosource() const

const vector< const CSeq_feat * > & FeatCDS()

vector< const CSeq_feat * > m_FeatMRNAs

map< const CRefNode *, CParseNode * > m_NodeMap

const vector< const CSeq_feat * > & FeatAll()

const vector< const CSeq_feat * > & FeatIntrons()

CRef< CSimpleTypeObject< string > > m_Current_Cit_sub_StringObj

CRef< CSeq_annot > m_AF_Seq_annot

static bool InNucProtSet(const CParseNode *node)

CConstRef< CSuspect_rule_set > m_OrganelleProductRules

CBioseq_EditHandle GetBioseqHandle(const CBioseq &bs)

vector< const CSeq_feat * > m_FeatTRNAs

const vector< const CSeq_feat * > & FeatRRNAs()

vector< const CSeq_feat * > m_FeatExons

CConstRef< CSeqdesc > GetMolinfo() const

CSeqdesc_vec GetSeqdesc()

const CBioseq_set & CurrentBioseq_set() const

const vector< const CSeq_feat * > & FeatMisc()

const CObject * GetMore(CReportObj &obj)

vector< CConstRef< CBioseq_set > > m_Bioseq_set_Stack

CRef< CSubmit_block > m_AF_Submit_block

CConstRef< CPub_equiv > m_Current_Pub_equiv

CConstRef< CSuspect_rule_set > m_ProductRules

void PropagateFlags(unsigned char f)

vector< const CSeq_feat * > m_FeatIntrons

vector< const CSeq_feat * > m_FeatPseudo

static bool IsSeqSet(EObjType n)

vector< const CSeq_feat * > m_FeatMisc

eTestTypes GetType() const override

virtual CRef< CAutofixReport > Autofix(CDiscrepancyObject *obj, CDiscrepancyContext &context) const =0

virtual void Visit(CDiscrepancyContext &context)=0

eTestNames GetName() const override

const CDiscrepancyCaseProps * m_props

CDiscrepancyCore(const CDiscrepancyCaseProps *props)

string_view GetSName() const override

TReportItemList m_ReportItems

virtual void Summarize()=0

string_view GetDescription() const override

const TReportItemList & GetReport() const override

CDiscrepancyItem(string_view title, const string &name, const string &msg, const string &xml, const string &unit, size_t count)

string_view GetTitle() const override

bool IsExtended() const override

size_t GetCount() const override

TReportObjectList & SetDetails()

TReportObjectList GetDetails() const override

bool IsInfo() const override

bool IsReal() const override

void SetAutofix(bool value)

bool IsFatal() const override

string GetUnit() const override

TReportItemList GetSubitems() const override

CDiscrepancyItem(const string &msg)

string GetStr() const override

string GetXml() const override

string GetMsg() const override

bool CanAutofix() const override

ESeverity GetSeverity() const override

bool IsSummary() const override

friend bool operator<(const CReportObjPtr &one, const CReportObjPtr &another)

CRef< CDiscrepancyContext::CRefNode > m_Ref

string GetBioseqLabel() const override

string GetPath() const override

void SetMoreInfo(CObject *data) override

string GetShort() const override

bool IsFixed() const override

bool CanAutofix() const override

CConstRef< CObject > m_More

CConstRef< CObject > GetMoreInfo()

string GetText() const override

CRef< CDiscrepancyContext::CRefNode > m_Fix

CRef< CDiscrepancyCore > m_Case

EType GetType() const override

CDiscrepancyObject(CDiscrepancyContext::CRefNode *ref, CDiscrepancyContext::CRefNode *fix=nullptr, const CObject *more=nullptr)

TDiscrepancyCoreMap m_Tests

void Visit(CDiscrepancyContext &context) override

CRef< CAutofixReport > Autofix(CDiscrepancyObject *, CDiscrepancyContext &) const override

void Summarize() override

CDiscrepancyPrivateData< _Name > m_private

static CRef< CDiscrepancyCore > Create()

@Pubdesc.hpp User-defined methods of the data storage class.

static void Add(TReportObjectList &list, TReportObjectSet &hash, CReportObj &obj, bool unique=true)

CReportNode(const string &name)

bool Exist(CReportObj &obj)

CReportNode & Merge(CReportNode &other)

CReportNode & Add(CReportObj &obj, bool unique=true)

CReportNode & NoRec(bool b=true)

map< string, CRef< CReportNode > > TNodeMap

CReportNode & Summ(bool b=true)

TReportObjectList & GetObjects()

CReportNode & Ext(bool b=true)

CReportNode & operator[](const string &name)

CReportNode & Severity(CReportItem::ESeverity s)

CRef< CReportItem > Export(CDiscrepancyCore &test, bool unique=true) const

CReportItem::ESeverity m_Severity

static bool Exist(TReportObjectSet &hash, CReportObj &obj)

bool Exist(const string &name) const

CReportNode & Add(TReportObjectList &objs, bool unique=true)

void Copy(CRef< CReportNode > other)

static CRef< CReportObj > Create(CRef< CDiscrepancyCore > disc_core, const CReportObj &obj, bool autofix)

namespace ncbi::objects::

Base class for all serializable objects.

const_iterator end() const

const_iterator find(const key_type &key) const

vector< CRef< CReportItem > > TReportItemList

vector< CRef< CReportObj > > TReportObjectList

CConstRef< objects::CSuspect_rule_set > GetProductRules(const string &name="")

CConstRef< objects::CSuspect_rule_set > GetOrganelleProductRules(const string &name="")

void UnitTest_FLATFILE_FIND()

Checking that FLATFILE_FIND.inc is in sync with kSpellFixes If the array is changed,...

map< eTestNames, CRef< CDiscrepancyCore > > TDiscrepancyCoreMap

list< pair< CRef< CDiscrepancyObject >, string > > TGenesList

CDiscrepancyContext - manage and run the list of tests.

set< CReportObjPtr > TReportObjectSet

map< string, TGenesList > TGeneLocusMap

#define ADD_DISCREPANCY_TYPE(type)

std::ofstream out("events_result.xml")

main entry point for tests

static const struct name_t names[]

#define test(a, b, c, d, e)

static int RunTests(void)

Code to iterate through all tests to run.

static const char location[]

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, EMissing action=eMissing_Default)

CBioseq_EditHandle GetBioseqEditHandle(const CBioseq &bioseq)

Get edit handle for the specified object Throw an exception if object is not found,...

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::streampos CNcbiStreampos

Portable alias for streampos.

#define NCBI_DISCREPANCY_EXPORT

const Tdata & Get(void) const

Get the member data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

const TData & GetData(void) const

Get the Data member data.

bool IsPub(void) const

Check if variant Pub is selected.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

const TTitle & GetTitle(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

bool IsPub(void) const

Check if variant Pub is selected.

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

const TPub & GetPub(void) const

Get the Pub member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

static string GetProductName(const CProt_ref &prot)

const GenericPointer< typename T::ValueType > T2 value

string GetLocusTag(const CSeq_feat &f, const LocMap &loc_map)

string GetProduct(const CProt_ref &prot_ref)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

const std::initializer_list< const char * > * Aliases

CConstRef< CSeqdesc > m_Molinfo

CParseNode & AddDescriptor(const CSeqdesc &seqdesc)

CConstRef< CSeqdesc > m_Title

vector< CRef< CParseNode > > m_Children

CParseNode(EObjType type, unsigned index, CParseNode *parent=nullptr)

map< const CBioSource *, CParseNode * > m_BiosourceMap

vector< const CBioSource * > m_Biosources

vector< CRef< CParseNode > > m_Features

void SetType(EObjType type)

bool InGenProdSet() const

vector< const CPubdesc * > m_Pubdescs

vector< CRef< CParseNode > > m_Descriptors

CConstRef< CSerialObject > m_Obj

CParseNode & AddFeature(const CSeq_feat &feat)

vector< CConstRef< CSeqdesc > > m_SetBiosources

map< const CSeq_feat *, CParseNode * > m_FeatureMap

CConstRef< CSeqdesc > m_Biosource

const CParseNode * m_Gene

map< const CSeqdesc *, CParseNode * > m_DescriptorMap

map< const CAuth_list *, CParseNode * > m_AuthorMap

shared_ptr< CSeqSummary > m_BioseqSummary

map< const CPubdesc *, CParseNode * > m_PubdescMap

CConstRef< CSeqdesc > GetBiosource() const

CConstRef< CSeqdesc > GetMolinfo() const

CConstRef< CSeqdesc > GetTitle() const

vector< const CAuth_list * > m_Authors

map< const CAuth_list *, const CPub * > m_AuthorPubMap

CRef< CRefNode > m_Parent

CRefNode(EObjType type, unsigned index)

const CSeq_feat & operator*()

vector< CRef< CParseNode > >::iterator it

bool operator!=(const iterator &x) const

bool operator==(const iterator &x) const

CSeq_feat_run(CParseNode &n)

bool operator==(const iterator &x) const

bool operator!=(const iterator &x) const

const CSeq_feat & operator*()

vector< CRef< CParseNode > >::iterator it

iterator(vector< CRef< CParseNode >>::iterator x)

CSeq_feat_vec(CParseNode &n)

bool operator==(const iterator &x) const

const CSeqdesc & operator*()

bool operator!=(const iterator &x) const

vector< CRef< CParseNode > >::iterator it

CSeqdesc_run(CParseNode &n)

iterator(vector< CRef< CParseNode >>::iterator x)

bool operator==(const iterator &x) const

vector< CRef< CParseNode > >::iterator it

bool operator!=(const iterator &x) const

const CSeqdesc & operator*()

CSeqdesc_vec(CParseNode &n)

friend bool operator<(const CReportObjPtr &one, const CReportObjPtr &another)

CReportObjPtr(const CReportObj *p)

vector< pair< size_t, size_t > > NRuns

size_t _CBposition[WINDOW_SIZE]

static const size_t WINDOW_SIZE

size_t _CBscore[WINDOW_SIZE]

CSimpleTypeObject(const T &v)

string GetTextObjectDescription(const CSeq_feat &sf, CScope &scope)

static CS_CONTEXT * context

void Merge(wxMenu &menu_1, const wxMenu &menu_2)

merges all items form menu_2 into menu_1, preserving the structure if possible

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