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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/discrepancy__core_8cpp_source.html below:

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

constexpr

num_test_cases =

(eTestNames::max_test_names);

= std::array<const CDiscrepancyCaseProps**, num_test_cases>;

<std::size_t... I>

{xGetProps<I>()...};

xAssembleArray(std::make_index_sequence<num_test_cases>{});

constexpr

autofix_names{DISC_AUTOFIX_TESTNAMES};

TAliasMap& GetAliasMap();

(

alias_name: *aliases) {

s_alias_map[alias_name] =

eTestNames

(

);

(name < eTestNames::max_test_names) {

(prop_ref && *prop_ref) {

std::out_of_range(

);

std::ostream&

(std::ostream&

, NDiscrepancy::eTestNames name)

(props.

== name)

eTestNames

(

);

eTestNames::notset;

vector<string_view> V;

V.reserve(alias_names->size());

(

rec: *alias_names)

(

tn:

) {

(props->sName[0] !=

&& (props->Group & group) == group) {

.set(props->Name);

& node =

[name];

(unique &&

.find(&obj) !=

.end()) {

(

& it : objs) {

(list,

, *it, unique);

<<

<<

.size() <<

<< other.

.size()

(

it: other.

) {

& rec =

[it.first];

rec->Merge(*it.second);

autofix =

;

(

& it :

) {

severity = it.second->m_Severity;

(severity < sub->GetSeverity()) {

(

& ob : details) {

(objs,

, *ob, unique);

(

& ob : objs) {

(ob->CanAutofix()) {

.erase(

, k -

+ 2);

=

.find(

);

(

!= string::npos) {

((

=

.find(

)) != string::npos) {

(

!= string::npos) {

((

=

.find(

)) != string::npos) {

unit =

.substr(0,

);

(0 ==

.find(

)) {

((

=

.find(

)) != string::npos) {

unit =

.substr(0,

);

item->m_Autofix = autofix;

item->m_Severity = severity;

item->m_Ext =

;

(

& rep : items) {

(

& obj : objs) {

(

& it : report_objs) {

ref = disc_obj.

();

disc_obj->

= disc_core;

disc_obj->

= ref;

ss =

; ss += e.

();

.erase(

, k -

+ 2);

(!fname.empty()) {

(pTypeInfo == CBioseq::GetTypeInfo()) {

(pTypeInfo == CBioseq_set::GetTypeInfo()) {

(pTypeInfo == CSeq_entry::GetTypeInfo()) {

(pTypeInfo == CSeq_submit::GetTypeInfo()) {

+ pTypeInfo->GetName());

&

= *tt.second;

severity = 0;

&

= *tt.second;

(

& rep :

.GetReport()) {

sev = rep->GetSeverity();

severity = sev > severity ? sev : severity;

(

it: other_ptr.m_Tests) {

(it.second && !it.second->Empty())

& current =

[it.first];

(current && !current->Empty())

current->Merge(*it.second);

CDiscrepancyContext::TestString(

&

)

(

& it :

) {

(

& tt :

) {

(

& tt :

) {

(

& tt :

) {

(!details.empty() || tt->GetCount() > 0) {

(

& ob : details) {

(tt->CanAutofix()) {

di->m_Autofix =

;

(tt->IsFatal()) {

(

& it :

) {

(

& it2 : list) {

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

->Call(*

);

<<

);

brk =

.find(

);

brk == string::npos ?

:

.substr(0, brk) +

+

.substr(brk + 1);

+ (

.empty() ?

:

);

+ (

.empty() ?

:

);

.empty() ?

:

+

;

.empty() ?

:

+

;

(node->m_Type ==

) {

brk = node->m_Text.find(

);

brk == string::npos ?

: node->m_Text.substr(0, brk);

vector<const CRefNode*>

,

;

reverse(

.begin(),

.end());

reverse(

.begin(),

.end());

=

(

.size(),

.size());

(

= 0;

<

;

++) {

(

[

] !=

[

]) {

(

[

]->m_Index !=

[

]->m_Index) {

[

]->m_Index <

[

]->m_Index;

.size() ==

.size() ? &*

< &*

:

.size() <

.size();

(

& tst :

) {

(

& it : list) {

(

& obj : it->GetDetails()) {

(obj->CanAutofix()) {

tofix.push_back(obj);

retval[rec.first] = rec.second;

static constexpr auto xGetProps()

static const TAliasMap & GetAliasMap()

static const TTestNamesSet & GetAutofixTests()

static constexpr TArray xAssembleArray(std::index_sequence< I... >)

static const CDiscrepancyCaseProps & GetProps(eTestNames name)

std::array< const CDiscrepancyCaseProps **, num_test_cases > TArray

static constexpr TArray PopulateTests()

vector< CDiscrepancyCore * > m_All_PUBDESC

vector< CDiscrepancyCore * > m_All_SUBMIT

vector< CDiscrepancyCore * > m_All_DESC

TDiscrepancyCaseMap GetTests() const override

void AddTest(eTestNames name) override

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

TDiscrepancyCoreMap m_Tests

void Push(const CSerialObject &root, const string &fname) override

CRef< CParseNode > m_RootNode

void ParseObject(const CBioseq &root)

vector< CDiscrepancyCore * > m_All_SEQ_SET

CRef< CParseNode > m_CurrentNode

vector< CDiscrepancyCore * > m_All_BIOSRC

unsigned Summarize() override

map< string, size_t > Autofix() override

CSeq_feat_run GetAllFeat()

static string TypeName(EObjType n)

void CollectFeature(const CSeq_feat &feat)

map< const CRefNode *, CParseNode * > m_NodeMap

static bool CompareRefs(CRef< CReportObj > a, CRef< CReportObj > b)

vector< CDiscrepancyCore * > m_All_FEAT

vector< CDiscrepancyCore * > m_All_STRING

vector< CDiscrepancyCore * > m_All_AUTHORS

static bool IsSeqSet(EObjType n)

vector< CDiscrepancyCore * > m_All_SEQUENCE

void Merge(CDiscrepancyCore &other)

virtual void Visit(CDiscrepancyContext &context)=0

TReportObjectList GetObjects() const override

TReportItemList m_ReportItems

const TReportItemList & GetReport() const override

void Call(CDiscrepancyContext &context)

vector< CRef< CDiscrepancyGroup > > m_List

TReportItemList Collect(TDiscrepancyCaseMap &tests, bool all=true) const

CDiscrepancyGroup(const string &name="", const string &test="")

TReportObjectList & SetDetails()

void SetAutofix(bool value)

static CDiscrepancyObject * CreateInternal(CDiscrepancyContext::CRefNode *ref, CRef< CDiscrepancyCore > disc_core, bool autofix)

CRef< CDiscrepancyContext::CRefNode > m_Ref

CReportObj * Clone(bool fix, CConstRef< CObject > data) const

CConstRef< CObject > m_More

CRef< CDiscrepancyContext::CRefNode > m_Fix

CRef< CDiscrepancyCore > m_Case

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

void Summarize() override

TDiscrepancyCoreMap m_Tests

void Merge(CDiscrepancyProduct &other) override

static CRef< CDiscrepancySet > New(objects::CScope &scope)

static std::atomic< bool > m_Gui

static string Format(const string &str, unsigned int count)

static CRef< CReportItem > Create(const string &test_name, const string &name, const CReportObj &main_obj, const TReportObjectList &report_objs, bool autofix=false)

virtual vector< CRef< CReportItem > > GetSubitems() const =0

virtual string GetUnit() const =0

virtual ESeverity GetSeverity() const =0

virtual TReportObjectList GetDetails() const =0

virtual bool CanAutofix() const =0

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

CReportNode & Merge(CReportNode &other)

CReportNode & operator[](const string &name)

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

CReportItem::ESeverity m_Severity

void Copy(CRef< CReportNode > other)

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

Base class for all serializable objects.

const_iterator begin() const

const_iterator find(const key_type &key) const

vector< CRef< CReportItem > > TReportItemList

vector< CRef< CReportObj > > TReportObjectList

eTestNames GetDiscrepancyCaseName(string_view name)

string_view GetDiscrepancyDescr(string_view name)

#define REGISTER_DISCREPANCY_TYPE(type)

TGroup GetDiscrepancyGroup(eTestNames name)

vector< string > GetDiscrepancyNames(TGroup group)

static CCaseRegistry::TAliasMap xPopulateAliases()

vector< string_view > GetDiscrepancyAliases(eTestNames name)

TTestNamesSet GetDiscrepancyTests(TGroup group)

std::ostream & operator<<(std::ostream &str, NDiscrepancy::eTestNames name)

static constexpr CCaseRegistry::TArray g_test_registry

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

main entry point for tests

bool Empty(const CNcbiOstrstream &src)

static const struct name_t names[]

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

static const char * str(char *buf, int n)

static DbTestEntry * tests

static char test_name[128]

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

#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.

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static const char label[]

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are BIOSEQ_INFO and BLOB_PROP at all

constexpr bool empty(list< Ts... >) noexcept

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

C++ I/O stream wrappers to compress/decompress data on-the-fly.

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

string GetBioseqLabel() const

CRef< CRefNode > m_Parent

static CS_CONTEXT * context

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