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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/discrepancy_8hpp_source.html below:

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

<eTestTypes _type>

= std::integral_constant<eTestTypes, _type>;

()

{

; }

vector<CRef<CAutofixReport>>

;

eSeverity_warning = 1,

<

Container>

AddTests(

Container& cont)

success =

;

for_each(cont.begin(), cont.end(), [

, &success](

&

) { success &= this->AddTest(test_name); });

Parse(

& root,

& fname =

) { Push(root, fname); Parse(); }

TestString(

&

) = 0;

eOutput_Summary = 1 << 0,

eOutput_Fatal = 1 << 1,

eOutput_Ext = 1 << 2,

eOutput_Files = 1 << 3

() {

m_Gui; }

* m_UserData =

;

vector<CRef<CDiscrepancyGroup> >

;

CAutofixReport(const string &s, unsigned int n)

vector< CRef< CAutofixReport > > V

const vector< CRef< CAutofixReport > > & GetSubitems()

void AddSubitems(const vector< CRef< CAutofixReport >> &v)

unsigned int GetN() const

virtual string_view GetDescription() const =0

virtual eTestTypes GetType() const =0

virtual string_view GetSName() const =0

virtual const TReportItemList & GetReport() const =0

virtual ~CDiscrepancyCase()

virtual TReportObjectList GetObjects() const =0

virtual eTestNames GetName() const =0

const CDiscrepancyGroup & operator[](size_t n) const

vector< CRef< CDiscrepancyGroup > > m_List

void Add(CRef< CDiscrepancyGroup > child)

virtual void OutputXML(CNcbiOstream &out, unsigned short flags)=0

virtual void Merge(CDiscrepancyProduct &other)=0

virtual void Summarize()=0

virtual void OutputText(CNcbiOstream &out, unsigned short flags, char group=0)=0

virtual CRef< CDiscrepancyProduct > RunTests(const TTestNamesSet &testnames, const CSerialObject &object, const string &filename)=0

virtual void AddTest(eTestNames name)=0

virtual void Autofix(TReportObjectList &tofix, map< string, size_t > &rep, const string &default_header=kEmptyStr)=0

virtual unsigned Summarize()=0

void * GetUserData() const

virtual void ParseStream(CObjectIStream &stream, const string &fname, bool skip, const string &default_header=kEmptyStr)=0

void SetLineage(const string &s)

void SetUserData(void *p)

virtual void AddTest(string_view name)=0

virtual void Push(const CSerialObject &root, const string &fname=kEmptyStr)=0

virtual map< string, size_t > Autofix()=0

static std::atomic< bool > m_Gui

virtual void SetSuspectRules(const string &name, bool read=true)=0

const string & GetLineage() const

static void SetGui(bool b)

virtual void ParseStrings(const string &fname)=0

virtual ~CDiscrepancySet()

virtual CRef< CDiscrepancyProduct > GetProduct()=0

virtual const CSerialObject * FindObject(CReportObj &obj, bool alt=false)=0

virtual TDiscrepancyCaseMap GetTests() const =0

virtual string_view GetTitle() const =0

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

virtual bool IsExtended() const =0

virtual bool IsSummary() const =0

virtual string GetStr() const =0

virtual string GetXml() const =0

virtual string GetUnit() const =0

virtual ESeverity GetSeverity() const =0

virtual TReportObjectList GetDetails() const =0

virtual bool CanAutofix() const =0

virtual string GetMsg() const =0

virtual bool IsInfo() const =0

virtual bool IsFatal() const =0

virtual bool IsReal() const =0

virtual size_t GetCount() const =0

virtual string GetFeatureType() const =0

virtual string GetBioseqLabel() const =0

virtual string GetLocation() const =0

virtual string GetPath() const =0

virtual string GetProductName() const =0

virtual bool IsFixed() const =0

virtual bool CanAutofix() const =0

virtual string GetLocusTag() const =0

virtual EType GetType() const =0

virtual void SetMoreInfo(CObject *data)=0

virtual string GetShort() const =0

virtual string GetText() const =0

namespace ncbi::objects::

Base class for all serializable objects.

Include a standard set of the NCBI C++ Toolkit most basic headers.

bool IsShortrRNA(const objects::CSeq_feat &f, objects::CScope *scope)

vector< CRef< CReportItem > > TReportItemList

vector< CRef< CReportObj > > TReportObjectList

TGroup GetDiscrepancyGroup(eTestNames name)

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

eTestNames GetDiscrepancyCaseName(string_view)

vector< string_view > GetDiscrepancyAliases(eTestNames name)

TTestNamesSet GetDiscrepancyTests(TGroup group)

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

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

std::integral_constant< eTestTypes, _type > TTypeTag

NCBI_DISCREPANCY_EXPORT vector< string > GetDiscrepancyNames(TGroup group=EGroup::eAll)

string FixProductName(const objects::CSuspect_rule *rule, objects::CScope &scope, string &prot_name, GetFeatureFunc get_mrna, GetFeatureFunc get_cds)

map< eTestNames, CRef< CDiscrepancyCase > > TDiscrepancyCaseMap

string_view GetDiscrepancyDescr(eTestNames name)

std::function< CRef< objects::CSeq_feat >) > GetFeatureFunc

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

main entry point for tests

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

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

static DbTestEntry * tests

static char test_name[128]

#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.

#define NCBI_DISCREPANCY_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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